The transcription factor RIP140 regulates interferon γ signaling in breast cancer

RIP140 (receptor interacting protein of 140 kDa) is an important player in breast cancer (BC) by regulating key cellular pathways such as nuclear hormone receptor signaling. In order to identify additional genes specifically regulated by RIP140 in BC, we performed a transcriptomic analysis after silencing its expression in MCF-7 cells. We identified the interferon γ (IFNγ) signaling as being substantially repressed by RIP140 knockdown. Using the GBP1 (guanylate binding protein 1) gene as a reporter of IFNγ signaling, we demonstrated its robust induction by RIP140 through an ISRE motif, leading to a significant reduction of its induction upon IFNγ treatment. Furthermore, we showed that low levels of RIP140 amplified the IFNγ-dependent inhibition of BC cell proliferation. In line with these data, reanalysis of transcriptomic data obtained in human BC samples revealed that IFNγ levels were associated with good prognosis only for BC patients exhibiting tumors expressing low levels of RIP140, thus confirming its effect on the anti-tumor activity of IFNγ provided by our experimental data. Altogether, this study identifies RIP140 as a new regulator of IFNγ signaling in breast tumorigenesis.

Blocking the Dkk1-LRP6 interaction prevents acute amyloid-β-driven cognitive impairment

Synapse loss driven by amyloid-β (Aβ) is an early event in Alzheimer's disease (AD). Although the mechanism by which Aβ drives synapse loss remain poorly understood data indicate that a disruption of Wnt signalling plays an important part. We have shown that Aβ exerts its effects on synapses through Dickkopf-1 (Dkk1), a secreted protein that acts upon Wnt signalling via a direct interaction with the canonical Wnt pathway co-receptor proteins, LRP5 and LRP6, preventing their interaction with the receptor Frizzled. This antagonises canonical, Wnt/β-catenin, signalling and allows concomitant activation of non-canonical signalling pathways. We contend that it is the switch from canonical to non-canonical Wnt signalling activity that drives synapse loss and subsequent cognitive impairment in AD, driven by Aβ and mediated by Dkk1. Preventing the Dkk1-LRP5/6 interaction could protect synapses and cognition against Aβ by maintaining canonical Wnt signalling. To test this, we mapped the Dkk1-LRP6 interaction by peptide array and identified a small peptide able to disrupt the Dkk1-LRP6 interaction. This Dkk1-LRP6 'disruptor' peptide dose dependently restores canonical Wnt signalling in the presence of Dkk1; blocks Dkk1-driven dendritic spine loss in primary rat cortical cultures and the accompanying increase in endogenous Aβ production; and when administered intracerebroventricularly to a rat acute Aβ model, blocks Aβ-driven cognitive impairment. These data support our contention that the ability of Aβ to induce Dkk1 and the effects of Dkk1 on LRP6 are an important element in AD aetiopathology and establish Dkk1 as a therapeutic target for protecting synapse and cognition in AD.

Dynamics and role of covalently-closed circular RNAs in Alzheimer's disease: A review of experimental and bioinformatics studies

Alzheimer's disease (AD) is an age-associated disorder characterized by cognitive decline, with dementia representing the final stage of a complex clinical-biological process rather than simply a more severe form of cognitive decline. Circular RNAs (circRNAs), novel non-coding RNAs, have emerged as key regulators of brain function and associated disorders. This study explores the role of circRNAs in AD by reviewing experimentally validated circRNAs in human and animal models. We identified 10 human (seven pathogenic, three protective) and six animal (three pathogenic, three protective) AD-related circRNAs. Experimental studies have confirmed that human protective circRNAs are predominantly downregulated in AD, where they function by sequestering specific miRNAs within cells, particularly miR-7, miR-142-5p, and miR-217, which have well-recognized neuroinflammatory functions. In-silico analysis revealed that circLPAR1 (pathogenic), circHUWE1 (pathogenic), and circHOMER1 (protective) interact with miRNAs that mainly control AD-related genes. Notably, circHOMER1 plays a key role in regulating multiple AD-related pathways, including autophagy, apoptosis, and PI3K-AKT and amyloid fiber formation. Furthermore, circRNA/protein interaction analysis revealed that circHUWE1 predominantly associates with RNA transport proteins, whereas circHOMER1 interacts with proteins involved in mRNA surveillance pathways. Remarkably, docking analysis demonstrated that circAβ-a (pathogenic) exhibits a strong affinity for eukaryotic translation initiation factor 4A3 protein, while circHOMER1 shows a higher binding affinity for DGCR8 microprocessor complex subunit protein. Our study presents a concise list of circRNAs as potential key targets for further investigation in AD research. Future experimental research is essential to uncover their precise mechanisms and assess their potential as biomarkers, offering promising avenues for developing interventions to alleviate cognitive decline in AD.

The arginine metabolism and its deprivation in cancer therapy

Arginine deprivation has emerged as a promising therapeutic strategy in cancer treatment due to the auxotrophy of certain tumors. Many cancers, such as pancreatic, colorectal, and hepatocellular carcinoma, exhibit downregulated argininosuccinate synthetase, making them reliant on external arginine sources. This dependency allows targeted therapies that deplete arginine, inhibiting tumor growth while sparing normal cells. Arginine is crucial for various cellular processes, including protein synthesis and immune function. Its deprivation affects both tumor metabolism and immune responses, potentially enhancing cancer therapy. Studies have explored using enzymes like arginine deiminase and arginase, often modified for increased stability and reduced immunogenicity, to effectively lower arginine levels in the tumor microenvironment. These approaches show promise, particularly in tumors with low argininosuccinate synthetase expression. However, the impact on immune cells and the potential for resistance highlight the need for further research. Combining arginine deprivation with other treatments might improve outcomes, offering a novel approach to combat arginine-dependent cancers.

Ferroptosis meets inflammation: A new frontier in cancer therapy

Ferroptosis, an iron-dependent form of regulated cell death driven by lipid peroxidation, has emerged as a critical player in cancer pathogenesis. Concurrently, inflammation, a key biological response to tissue injury or infection, significantly influences cancer development and progression. The interplay between ferroptosis and inflammation represents a promising yet underexplored area of research. This review synthesizes recent advances in understanding the molecular mechanisms governing their interaction, emphasizing how ferroptosis triggers inflammatory responses and how inflammatory mediators, such as TNF-α, regulate ferroptosis through iron metabolism and lipid peroxidation pathways. Key molecular targets within the ferroptosis-inflammation axis, including GPX4, ACSL4, and the NF-κB signaling pathway, offer therapeutic potential for cancer treatment. By modulating these targets, it may be possible to enhance ferroptosis and fine-tune inflammatory responses, thereby improving therapeutic outcomes. Additionally, this review explores the broader implications of targeting the ferroptosis-inflammation interplay in disease treatment, highlighting opportunities for developing innovative strategies to combat cancer. By bridging the gap in current knowledge, this review provides a comprehensive resource for researchers and clinicians, offering insights into the therapeutic potential of this intricate biological relationship.

The intersections between neuroscience and medulloblastoma

Medulloblastoma (MB) represents the most common malignant central nervous system tumor in childhood. The nervous system plays a critical role in the progression of MB, with interactions between the nervous system and cancer significantly influencing oncogenesis, tumor growth, invasion, stemness, and metabolism. These interactions also regulate angiogenesis, metastatic dissemination, the tumor immune microenvironment, and drug resistance. Investigating the nervous system-MB axis holds promise for identifying diagnostic markers, prognostic biomarkers, and therapeutic targets. It also provides insights into the molecular mechanisms underlying MB and informs the development of novel therapeutic strategies. This review summarizes the latest advancements in understanding the interplay between the nervous system and MB, including the role of glial cells in MB and the potential of drug repurposing targeting nervous system components for MB treatment. These findings underscore promising diagnostic and therapeutic opportunities for MB management. Additionally, we outline future research directions in neurosciences that may pave the way for innovative therapeutic approaches and deepen our understanding of this complex disease.

Analysis of germline-somatic mutational connections in colorectal cancer reveals differential tumorigenic patterns and a novel predictive marker for germline mutation carriers

Colorectal cancer (CRC) genetic testing of regions beyond clinical guidelines has revealed a substantial number of likely pathogenic germline mutations (GMs). It remains largely undetermined whether and how these GMs, typically located in non-mismatch repair (non-MMR) genes, are associated with the tumorigenesis of CRC. This study aimed to identify CRC-predisposing GMs among 93 cancer susceptibility genes and investigate their potential influences on CRC somatic mutational features. We secondarily aimed to investigate whether somatic ERBB2 amplification contributes to identifying GM carriers. This study incorporated a total of 3,240 Chinese CRC patients and 10,588 control individuals. CRC patients were subjected to paired tumor-normal sequencing with a 1,021-gene panel. A case-control analysis was conducted to profile the GM-associated CRC risk. A comprehensive germline-somatic association analysis was performed among 2,405 patients, with key findings subsequently validated in an independent 835-patient cohort and the TCGA CRC cohort. The case-control results supported CRC-predisposing effects of GMs in certain homologous recombination repair (HRR) and DNA damage checkpoint factor (CPF) genes, such as BRCA1/2, RecQ helicase genes, ATM, and CHEK2. HRR GMs were associated with an increased copy number alteration burden, more TP53 clonal mutations, and a higher probability of carrying somatic ERBB2 amplification. CPF GMs were inferred to have synergistic effects with ARID1A and KDM6A somatic mutations in CRC tumorigenesis. Among patients with onset age ≥55 years, stable microsatellites, and no cancer family history, ERBB2 amplification was significantly predictive of GM carriers. Our findings elucidate different germline tumorigenic patterns not driven by deficient MMR. Somatic ERBB2 amplification in CRC can serve as an indicator for germline genetic testing when traditional risk features are absent.

Decoding glioblastoma's diversity: Are neurons part of the game?

Glioblastoma multiforme (GBM, WHO Grade 4) is a highly aggressive primary brain tumor with limited treatment options and a poor prognosis. A key challenge in GBM therapy lies in its pronounced heterogeneity, both within individual tumors (intratumoral) and between patients (intertumoral). Historically, neurons have been underexplored in GBM research; however, recent studies reveal that GBM development is closely linked to neural and glial progenitors, often mimicking neurodevelopmental processes in a dysregulated manner. Beyond damaging neuronal tissue, GBM actively engages with neurons to promote pro-tumorigenic signaling, including neuronal hyperexcitability and seizures. Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of the tumor microenvironment (TME), uncovering the critical roles of immune cells, endothelial cells, and astrocytes in tumor progression. However, technical limitations of scRNA-seq hinder its ability to capture the transcriptomes of neurons, necessitating the use of single-nucleus RNA sequencing (snRNA-seq) to study these interactions at single-cell resolution. This work collects the emerging insights of glioblastoma-neuron interactions, focusing on how GBM exploits neurodevelopmental pathways and reshapes neuronal networks. Moreover, we perform bioinformatic analysis of publicly available snRNA-seq datasets to propose putative cell-cell interactions driving glioma-neuronal dynamics. This study delineates key signaling pathways and underscores the need for further investigation to evaluate their potential as therapeutic targets.

Vestigial-like family member 1 (VGLL1): An emerging candidate in tumor progression

Vestigial-like family member 1 (VGLL1), a product of an X-linked gene (VGLL1), belongs to a family of transcriptional co-activators including VGLL2, VGLL3 and VGLL4. These proteins are called vestigial-like because of the structural and functional similarities with the Drosophila ortholog vestigial (vg). VGLL1 is usually expressed in human placenta, and has also been detected in many aggressive cancers. For this reason, it is called an onco-placental protein. It can bind and activate the TEA-domain containing transcription factors TEAD1-4, and the interaction is mediated through a conserved 'valine-x-x-histidine-phenylalanine' domain (VxxHF, x denotes any amino acid) present in VGLL1 protein. Prior studies indicate a pro-tumorigenic role for this protein in several cancers including carcinoma of the breast. This review aims at summarizing our present knowledge about the functions of VGLL1, and the mechanisms that regulate its expression in cancer.

IPMK depletion influences genome-wide DNA methylation

Inositol polyphosphate multikinase (IPMK) is emerging as a critical regulator of nuclear functions. While earlier studies in yeast and cell lines linked IPMK to gene expression, recent work reveals its role in modulating histone acetylation through the activation of histone deacetylases 1/3 (HDAC1/3). Interestingly, HDAC1/3 interact with DNA methyltransferase 1 (DNMT1), stabilizing DNMT1 and promoting DNA methylation. As an HDAC1/3 activator, IPMK may thereby influence DNA methylation dynamics. This study investigates how the genetic depletion of IPMK influences DNA methylation, though the role of its kinase activity remains untested. Using long-read Oxford nanopore sequencing, we conducted methylation analysis for >28 millions of CpG sites and discovered that IPMK deletion results in over 22,000 differentially methylated regions (DMRs). Integrating affected genes by DMRs and RNA-seq data, we found that 35 genes show an inverse correlation between methylation in promoter regions and gene expression. Pathway analysis revealed that genes related to tissue remodeling and hematopoiesis are affected. Notably, MMP14 and LIF showed significant methylation changes in promoter regions under IPMK deletion, resulting in decreased mRNA and protein expression. Collectively, this study identifies IPMK as a novel regulator of DNA methylation. While this study did not investigate the role of IPMK's kinase activity in regulating DNA methylation, future studies will determine whether IPMK's effects on DNA methylation are driven by its kinase activity or by kinase-independent mechanisms.

Genomic and cellular context-dependent expression of the human ELMO1 gene transcript variants

Engulfment and cell motility protein 1 (Elmo1) forms a complex with Dedicator of cytokinesis (Dock) 1-5 and promotes GTP-loading of Rac1, the major agent of cell movement. While the pathophysiological roles of Elmo1 have expanded from apoptotic cell engulfment to cancer, inflammation, diabetic nephropathy and cardiomyopathy, little information is available on its transcriptional regulation. Genome databases indicate at least five transcript variants for human ELMO1: the variants V1, V4 and V5 encode a full-length 727 aa protein, whereas V2 and V3 encode a truncated Elmo1 of 247 aa that lacks N-terminal domains. A CpG island promoter drives the major V1 transcript, while an LTR12 drives V5 in intron 1, one of the three LTR12 family of retroviral elements in ELMO1. In contrast, the short-forms V2 and V3 contain CAT-TATA type promoters. Examination of various cell lines by RT-qPCR designed to detect individual transcripts showed that basal transcriptions of the variants were very low to undetectable in cultured cells. However, treatments with Trichostatin A, a histone deacetylase inhibitor, or with 5-Aza-2'-deoxycytidine, a DNA methyl transferase inhibitor, significantly upregulated V1, V4, V5 and V2 expression in a cell line-specific manner, indicating that these transcripts are epigenetically regulated. Another LTR12D transposon in intron 13 also drives an unannotated transcript stimulated by these inhibitors. Finally, we found the levels of V2 transcripts in the mouse and human brain exceed those of V1, suggesting a brain-specific regulation and role of V2 protein.

Liver sinusoidal endothelial cells in hepatic fibrosis: opportunities for future strategies

Liver sinusoidal endothelial cells (LSECs) are highly specialized endothelial cells that form the interface between the hepatic vasculature and parenchymal cells, playing a crucial role in maintaining hepatic homeostasis. Under pathological conditions, LSECs undergo capillarization, marked by the loss of fenestrae and formation of a basement membrane, thereby impairing microcirculation and promoting fibrosis. Beyond capillarization, LSECs experience a spectrum of pathological changes-including angiogenesis, endothelial-to-mesenchymal transition (EndMT), autophagy, and senescence-all of which contribute to fibrogenesis through distinct molecular pathways. Moreover, LSECs orchestrate liver fibrotic remodeling through dynamic crosstalk with hepatic stellate cells (HSCs), hepatocytes, Kupffer cells, and immune cells, exerting both pro- and anti-fibrotic effects. This review comprehensively summarizes LSECs dysfunction in hepatic fibrosis, with a particular focus on intercellular communication and emerging therapeutic strategies. Elucidating the regulatory networks that govern LSECs behavior may uncover new opportunities for the diagnosis and treatment of chronic liver disease.

Engineered oncolytic virus OH2-FLT3L enhances antitumor immunity via dendritic cell activation

The combination of oncolytic viruses (OVs) with other immunotherapies, such as immunostimulatory therapies, is a current research hotspot; however, optimizing their therapeutic potential remains to be fully explored. Here, we designed a novel oncolytic herpes simplex virus 2 expressing Fms-like tyrosine kinase 3 ligand (OH2-FLT3L), which induces an antitumor cytotoxic T cell immune response by activating dendritic cells (DCs). We found that OH2-FLT3L specifically infects tumor cells, induces immunogenic cell death (ICD), and releases a large number of tumor-specific antigens, which bound to danger signals and facilitated antigenic cross-presentation by DCs, significantly enhancing T cell activation and function. Experimental results showed that OH2-FLT3L significantly increased the proportion of activated DCs, enhanced the antitumor immune response, and effectively converted "cold" tumors into "hot" tumors. In addition, when combined with anti-PD-1 antibody, OH2-FLT3L further enhanced therapeutic efficacy. In conclusion, OH2-FLT3L, as a novel oncolytic virus, demonstrates the potential to enhance antitumor immune responses through DC activation.

The multilayered control of acetylation during adenovirus-based immunotherapy of cancer

Adenoviruses are highly immunogenic agents that have shown promise first as gene delivery vectors and later as oncolytic viruses. Currently, oncolytic adenoviruses are featured in over 30% of cancer virotherapy clinical trials. Due to their effective cellular uptake and hijack of cellular machinery, replication-competent adenoviruses are promising therapeutic agents for treating a wide range of tumors. Adenoviral influence on host cell acetylome regulation has regained attention, as these viruses redirect or suppress acetylation during replication, making them potentially desirable therapeutic agents for cancers driven by epigenetic modifications. In this review, we aim to cover the viral processes influencing the acetylome of the host genome. In addition, we shall discuss the effect of differential acetylation on the antiviral defense mounted by the host immune system. Lastly, we will discuss the opportunities for combining acetylation modifiers with oncolytic adenoviruses to improve further outcomes for patients treated with viroimmunotherapy.

Preclinical study of microphthalmia-associated transcription factor inhibitor ML329 in gastrointestinal stromal tumor growth

Gastrointestinal stromal tumors (GISTs) comprise about 80% of mesenchymal neoplasms in the gastrointestinal tract. Although imatinib mesylate is the preferred treatment, the development of drug resistance highlights the need for novel therapeutic strategies. Recently, we have identified the microphthalmia-associated transcription factor (MITF) as a critical player in pro-survival signaling and tumor growth. This study investigates the effects of MITF inhibition using ML329, an MITF pathway inhibitor, on GIST cell viability in vitro and in NMRI-nu/nu mouse xenograft models. ML329 suppresses growth in imatinib-sensitive (GIST-T1) and -resistant (GIST 430/654) cell lines, impairs MITF targets such as BCL2 and CDK2, and induces S-G2/M cell-cycle arrest. In vivo, ML329 is well tolerated and significantly reduces tumor growth in established imatinib-sensitive and -resistant GIST models. These findings underscore the importance of MITF in GIST growth and support its inhibition as a promising therapeutic approach.

Deep Mutational Scanning of an Engineered High-affinity Ligand of the poly(A) Binding Protein MLLE Domain

The MLLE domain is a peptide-binding domain found in the poly(A) binding protein (PABP) and the ubiquitin protein E3 ligase N-recognin 5 (UBR5) that recognizes a conserved motif, named PABP-interacting motif 2 (PAM2). The majority of PAM2 sequences bind to MLLE domains with low-micromolar affinity. Here, we designed a chimeric PAM2 peptide termed super PAM2 (sPAM2) by combining classical and trinucleotide repeat-containing 6 (TNRC6)-like binding modes to create a superior binder for the MLLE domain. The crystal structure of the PABPC1 MLLE-sPAM2 complex shows a crucial role of conserved sPAM2 leucine, phenylalanine and tryptophan residues in the interaction. We used deep mutational scanning (DMS) coupled with isothermal titration calorimetry (ITC) to characterize the specificity profiles for PABPC1 and UBR5 MLLE. The best sPAM2 sequence binds to PABPC1 MLLE with low-nanomolar affinity and nearly 20-fold more tightly than the best natural PAM2 sequence. This suggests that the affinities of natural PAM2 sequences are tuned to control their binding to PABPC1 and UBR5. Our study will aid in the discovery of new PAM2-containing proteins (PACs) and facilitate in vivo studies of PAM2-mediated cellular pathways.

Novel_circ_0004013 targeting miR-29a-3p affects age-related hearing loss in miR-29a mouse model by RNA-seq analysis

Age-related hearing loss (ARHL) is a gradual, symmetrical sensorineural disorder. Exploring the pathogenesis of ARHL from a biological perspective is important for its treatment. In this study, we analyzed the circRNA expression profiles of 2-month-old miR-29a+/+ mice and miR-29a-/- mice by transcriptome sequencing to investigate the role of circRNAs in ARHL. We identified 12 differentially expressed circRNAs in the two groups. Our focus was on circRNAs predicted to regulate miR-29a, with novel_circ_0004013 identified as having a targeted binding relationship with miR-29a-3p. Dual luciferase assays confirmed that miR-29a-3p is a direct target of novel_circ_0004013. Fluorescence in situ hybridization (FISH) was employed to localize the novel_circ_0004013 in HEI-OC1 cells and the cochlea. Novel_circ_0004013 was mainly expressed in the cytoplasm. In the hair cells (HCs) and stria vascularis (SV) regions of miR-29a-/- mice, novel_circ_0004013 expression was higher than the corresponding regions in miR-29a+/+ mice. Furthermore, Western blot assays revealed that levels of oxidative stress and apoptosis were significantly decreased in HEI-OC1 cells following the knockdown of novel_circ_0004013, whereas these levels were significantly increased in HEI-OC1 cells after the knockdown of miR-29a-3p. It was indicated in rescue assays that novel_circ_0004013 expedited oxidative stress and apoptosis of HEI-OC1 cells via modulation on miR-29a-3p. These findings may reveal the important role of novel_circ_0004013 in hearing loss and provide a new perspective and theoretical basis for the molecular mechanism of ARHL.

DNA hypermethylation of MED1 and MED23 as early diagnostic biomarkers for unsolved issues in atrial fibrillation

BACKGROUND

Atrial fibrillation (AF) is the most common cardiac arrhythmia worldwide. Much effort was spent to identify biomarkers useful to stratify AF patients. Mediator complex (MED) is an ancestral regulator of transcriptional mechanisms. Here, we investigated the role of methyl DNA-MED regulatory networks in AF patients.

METHODS

We analyzed the methylome of circulating CD4+T lymphocytes isolated from patients at the time of first AF diagnosis vs. healthy subjects for identifying epigenetic dysregulation of MED-related genes.

RESULTS

We identified 10 differentially methylated regions (DMRs) which were hypermethylated and annotated to 10 genes encoding for MED complex subunits in CD4+T lymphocytes of AF patients vs. healthy subjects (HS). Network-oriented analysis prioritized 6 subunits including MED1, MED13, MED15, MED17, MED23 and MED30, which enriched significantly lipid metabolism pathways and cardiopathy onset. ROC curve analysis showed that elevated methylation levels of MED1 and MED23 discriminated AF patients with an area under the curve (AUC) of 92.7 % (p < 0.001) and an AUC = 100 % (p < 0.001), respectively. Methylation levels of MED23 correlated with the presence of mitral valve disease (p < 0.05) and NT-proBNP (p < 0.05); moreover, MED23 had a not inferior diagnostic value than circulating levels of NT-proBNP (AUC = 0.923, p < 0.001).

CONCLUSIONS

For the first time, we showed that DNA methylation changes are associated with regulation of MED complex subunits in early diagnosis of AF patients. Clinically, MED1 and MED23 hypermethylation showed a diagnostic value not inferior to circulating levels of NT-proBNP suggesting early diagnostic biomarker pathogenic molecular routes underlying disease onset.

Ginsenoside Rd and chrysophanol: Modulating the serine-glycine-one-carbon pathway to enhance neuroprotection in intracerebral hemorrhage

BACKGROUND

Intracerebral hemorrhage (ICH) is a devastating neurological disorder characterized by oxidative stress, inflammatory cascades, and metabolic dysregulation. Ginsenoside Rd (G-Rd) and chrysophanol (Chr), two natural compounds with antioxidative and anti-inflammatory properties, have demonstrated neuroprotective potential, however, their mechanisms in ICH remain unclear.

OBJECTIVE

This study aimed to investigate the protective effects of G-Rd and Chr against heme-induced injury in HT22 cells and in a rat model of ICH, with a focus on oxidative stress, inflammation, apoptosis, and metabolic regulation.

METHODS

In vitro, HT22 cells were exposed with heme (10 μmol/L, 12 h) to simulate ICH injury, followed by treatment with G-Rd and Chr (80 μmol/L). Reactive oxygen species (ROS), apoptosis, mitochondrial membrane potential, and inflammatory cytokines (TNF-α, IL-1β, IL-6, IL-10) were assessed using flow cytometry, fluorescence microscopy, and ELISA. In vivo, ICH was induced in rats via collagenase injection. Neurological function, hematoma volume, histopathology, and metabolic enzymes (SOD, MDA, NAD+, Ca2+-ATPase) were evaluated. Western blotting was used to analyze key enzymes in the serine-glycine-one‑carbon (SGOC) pathway.

RESULTS

G-Rd and Chr significantly suppressed ROS production (P < 0.05), downregulated pro-inflammatory cytokines (TNF-α, IL-1β, IL-6; P < 0.01), and inhibited apoptosis (P < 0.01) in HT22 cells. Both compounds restored mitochondrial membrane potential and alleviated cellular damage. In the ICH rat model, combined treatment improved neurological scores by 45 % (P < 0.01), decreased hematoma volume by 38 % (P < 0.01), and restored metabolic homeostasis through modulation of SGOC pathway enzymes (PHGDH, PSAT1, PSPH, SHMT2; P < 0.05). Synergistic effects were observed in both hematoma resolution and neuroprotection.

CONCLUSION

G-Rd and Chr confer neuroprotection in ICH through antioxidative, anti-inflammatory, anti-apoptotic, and metabolic regulatory mechanisms. Their synergistic efficacy underscores their promise as therapeutic candidates, meriting further investigation of their molecular targets and translational potential.

miR-660: A novel regulator in human cancer pathogenesis and therapeutic implications

MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression. Among these, miR-660, located on chromosome Xp11.23, is increasingly studied for its role in cancer due to its abnormal expression in various biological contexts. It is regulated by 8 competing endogenous RNAs (ceRNAs), which adds complexity to its function. miR- 660 targets 19 genes involved in 6 pathways such as PI3K/AKT/mTOR, STAT3, Wnt/β-catenin, p53, NF‑κB, and RAS, influencing cell cycle, proliferation, apoptosis, and invasion/migration. It also plays a role in resistance to chemotherapies like cisplatin, gemcitabine, and sorafenib in lung adenocarcinoma (LUAD), pancreatic ductal adenocarcinoma (PDAC), and hepatocellular carcinoma (HCC), thus highlighting its clinical importance. Additionally, leveraging liposomes as nanocarriers presents a promising avenue for enhancing cancer drug delivery. Our comprehensive study not only elucidates the aberrant expression patterns, biological functions, and regulatory networks of miR-660 and its ceRNAs but also delves into the intricate signaling pathways implicated. We envisage that our findings will furnish a robust framework and serve as a seminal reference for future investigations of miR-660, fostering advancements in cancer research and potentially catalyzing breakthroughs in cancer diagnosis and treatment paradigms.

SIRT2 alleviates pre-eclampsia via prompting mitochondrial biogenesis and function

AIMS

Pre-eclampsia (PE) globally impacts 2-8 % of pregnancies and is a leading cause of neonatal and maternal morbidity and mortality. Recent studies found the association between mitochondrial dysfunction and deficient motility of trophoblast cells in PE. Lower expressions of mitochondrial biogenesis related proteins (i.e. PGC1α, NRF1 and TFAM) and SIRT2 have recently been found. However, the regulative role of SIRT2 on the protein expression and acetylation of PGC1α and its influence on trophoblast migration and invasion in PE have never been investigated.

MATERIALS AND METHODS

The alterations in protein expressions of SIRT2 and PGC1α/NRF1/TFAM were examined in the placenta from pregnant women with and without PE. The role of SIRT2 on mitochondrial biogenesis and mitochondrial morphology/function was explored in trophoblast cell, and the findings were confirmed in the LPS-induced PE mice with adeno-associated virus transfection system.

KEY FINDINGS

We demonstrated the lower protein expressions of SIRT2 and PGC1α/NRF1/TFAM and mitochondrial dysfunction in PE patients and mice compared with counterparts. Moreover, overexpression of SIRT2 enhanced the protein expressions of PGC1α and deacetylated PGC1α, and further facilitating mitochondrial function and motility of trophoblast cells. In vivo, overexpression of SIRT2 attenuated the PE-like symptoms and adverse pregnancy outcomes in LPS-induced PE mice via promoting mitochondrial biogenesis.

SIGNIFICANCE

Above findings suggest that SIRT2 might be a potential interventive target against PE via improving deacetylation of PGC1α and mitochondrial biogenesis and function.

Glymphatic system dysfunction in adult ADHD: Relationship to cognitive performance

OBJECTIVES

While attention-deficit/hyperactivity disorder (ADHD) persists into adulthood, the relationship between glymphatic system function and cognitive performance in adult ADHD remains unclear. This study investigated the association between glymphatic system markers and cognitive outcomes in adults with ADHD.

METHODS

This case-control study includes 41 adults with ADHD and 108 age-matched healthy controls (HCs). Glymphatic function was evaluated using choroid plexus volume (CPV), diffusion tensor imaging along the perivascular space (DTI-ALPS) index and coupling between blood‑oxygen-level-dependent signals and cerebrospinal fluid signals (BOLD-CSF coupling). Cognitive performance was measured using standardized neuropsychological tests.

RESULTS

Compared with HCs, adults with ADHD exhibited significantly lower bilateral and whole-brain ALPS indices (P < 0.05). Although CPV was increased in the ADHD group, this difference did not reach statistical significance, and no significant differences were observed in BOLD-CSF coupling between the two groups. Furthermore, whole-brain ALPS indices were positively associated with visual memory performance (r = 0.422, P = 0.005), an effect that was more pronounced in the right hemisphere (r = 0.458, P = 0.002).

LIMITATIONS

The cross-sectional design limits causal inferences, and the effects of medication were not fully accounted for.

CONCLUSIONS

These findings identify an association between glymphatic dysfunction and cognitive impairment in adults with ADHD. The observed correlation suggests that alterations in glymphatic function may underlie ADHD-related cognitive deficits. Targeting these pathways could provide novel therapeutic opportunities in the management of adult ADHD.

Eeyarestatin I (ESI)-induced ERAD inhibition exhibits anti-cancer activity through multiple mechanisms in human colorectal cancer cells

Endoplasmic reticulum (ER)-associated degradation (ERAD) is a cellular process for maintenance of protein homeostasis in the ER and aberration of ERAD regulation leads to abnormal function of ER. As an inhibitory compound to ERAD, Eeyarestatin I (ESI) exhibits anti-cancer activity. In this study, we elucidated the anti-cancer mechanisms of ESI-induced ERAD inhibition in human colorectal carcinoma cells. Cellular viability of three different types of human colorectal cancer cells decreased in a dose-dependent manner by treatment with ESI. Treatment of ESI to human colorectal cancer cells led to significant increase of ubiquitin accumulation, G2/M phase cell cycle arrest, apoptosis, ER stress and autophagy. In addition, ESI treatment reduced transcriptional activity of nuclear factor kappa B (NF-κB), and increased phosphorylation of c-Jun NH2-terminal kinase (JNK) and intracellular production of reactive oxygen species (ROS). Decrease of cell viability and ROS release were JNK-dependent and apoptosis was ROS-dependent. On the other hand, treatment of the cells with ESI downregulated the expression of translocon-associated protein (TRAP) subunits including TRAPα, β, γ and δ, which was JNK- and ROS-dependent. In summary, ESI-induced ERAD inhibition triggers ER stress, G2/M cell cycle arrest, ROS-dependent apoptosis, and autophagy in human colorectal cancer cells. We are the first to identify TRAPs as novel target ER membrane proteins that are downregulated by ERAD inhibition in human colorectal cancer cells.

Fisetin and resveratrol exhibit senotherapeutic effects and suppress cellular senescence in osteoarthritic cartilage-derived chondrogenic progenitor cells

Chondrogenic progenitor cells (CPCs) in the articular cartilage of knee osteoarthritis (OA) patients exhibit cellular senescence and its associated secretory phenotype (SASP). We hypothesized that the senescence of CPCs can be suppressed using natural compounds. This study aimed to evaluate the senotherapeutic effects of fisetin and resveratrol to suppress the cellular senescence in CPCs. In vitro, pre-treatment of CPCs with increasing doses of fisetin and resveratrol (5μM-100μM) were non-cytotoxic, decreased the senescence index and dampened the expression of cellular senescence markers, p53 and p38MAPK. Additionally, SASP-related genes and proteins (MMP-9, MMP13) and inflammatory mediators (IL-1β, TGF-β, and IL-6) were downregulated. Further, in silico analysis confirmed the high binding affinity of these natural drugs to OA-related proteins. Overall, fisetin and resveratrol dampened the senescence of CPCs by downregulating the p53 effector protein and effectively reducing the SASP. From this study, natural compound candidates proved to be potential drug candidates that suppress senescence via p53.

Effects of decrease in Klotho protein expression on insulin signaling and levels of proteins related to brain energy metabolism

Mutations in Klotho have been associated with premature ageing and cognitive dysfunction. Although highly expressed in specific regions of the brain, the actions of Klotho in the central nervous system (CNS) remain largely unknown. Here, we show that animals with a mutated hypomorphic Klotho gene have altered glycaemic regulation, suggesting higher insulin sensitivity. In the CNS, pathways related to insulin intracellular signalling were found to be up-regulated in the hippocampus, with higher activation of protein kinase B and mammalian target of rapamycin and inactivation of the transcription factors forkhead box O (FOXO)-1 and FOXO-3a. In addition, the present study showed that in the hippocampi of wild-type aged mice, where Klotho is naturally downregulated, the levels of some proteins related to energy metabolism and metabolic coupling between neurones and astrocytes, such as monocarboxylate transporter 2 and 4, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase isoform 3 and lactate dehydrogenase enzymes isoforms A and B were altered. These findings suggest that Klotho plays an essential role in regulating proteins and genes related to metabolic coupling in the brain.

Unveiling EIF5A2: A multifaceted player in cellular regulation, tumorigenesis and drug resistance

The eukaryotic initiation factor 5A2 gene (EIF5A2) is a highly conserved and multifunctional gene that significantly influences various cellular processes, including translation elongation, RNA binding, ribosome binding, protein binding and post-translational modifications. Overexpression of EIF5A2 is frequently observed in multiple cancers, where it functions as an oncoprotein. Additionally, EIF5A2 is implicated in drug resistance through the regulation of various molecular pathways. In the review, we describe the structure and functions of EIF5A2 in normal cells and its role in tumorigenesis. We also elucidate the molecular mechanisms associated with EIF5A2 in the context of tumorigenesis and drug resistance. We propose that the biological roles of EIF5A2 in regulating diverse cellular processes and tumorigenesis are clinically significant and warrant further investigation.

ENsiRNA: A Multimodality Method for siRNA-mRNA and Modified siRNA Efficacy Prediction Based on Geometric Graph Neural Network

With the rise of small interfering RNA (siRNA) as a therapeutic tool, effective siRNA design is crucial. Current methods often emphasize sequence-related features, overlooking structural information. To address this, we introduce ENsiRNA, a multimodal approach utilizing a geometric graph neural network to predict the efficacy of both standard and modified siRNA. ENsiRNA integrates sequence features from a pretrained RNA language model, structural characteristics, and thermodynamic data or chemical modifications to enhance prediction accuracy. Our results indicate that ENsiRNA outperforms existing methods, achieving over a 13% improvement in Pearson Correlation Coefficient (PCC) for standard siRNA across various tests. For modified siRNA, despite challenges associated with RNA folding methods, ENsiRNA still demonstrates competitive performance in different datasets. This novel method highlights the significance of structural information and multimodal strategies in siRNA prediction, advancing the field of therapeutic design.

Therapeutic potential of Baicalin against experimental obsessive compulsive disorder: Evidence from CSF, blood plasma, and brain analysis

Obsessive-Compulsive Disorder (OCD) is a complex neuropsychiatric condition characterized by recurrent obsessions and compulsions, significantly impacting an individual's functionality and quality of life. This study aimed to explore the neuroprotective and therapeutic potential of baicalin, a flavonoid with known antioxidant, anti-inflammatory, and neurotropic properties, in an animal model of OCD induced by 8-OH-DPAT (8HPAT). The research utilized in silico docking studies and in vivo experiments to assess baicalin's interactions with key intracellular targets: SIRT-1, Nrf2, HO-1, and PPAR-gamma, and its effects on neurochemical, neurobehavioral, and histopathological parameters. In silico results indicated a strong binding affinity of baicalin for SIRT-1, Nrf2, HO-1, and PPAR-gamma, suggesting potential regulatory roles in antioxidant and anti-inflammatory pathways. In-vivo findings demonstrated that baicalin, administered at doses of 50 mg/kg and 100 mg/kg, significantly alleviated OCD-like behaviours, including excessive lever pressing, marble burying, and compulsive checking. Baicalin treatment normalized serotonin and dopamine levels and reduced glutamate levels in the brain, restoring neurotransmitter balance. Furthermore, baicalin decreased inflammatory cytokines (TNF-alpha and IL-1 beta), improved complete blood count profile, and gross morphological and histopathological alterations by restoring neuronal density and cellular integrity in affected brain regions. Combining baicalin with fluvoxamine (10 mg/kg) showed synergistic effects, further enhancing neuroprotective outcomes. These results suggest that baicalin holds promise as a potential therapeutic agent for OCD, warranting further clinical investigation to explore its efficacy and underlying mechanisms in human subjects. The findings underscore the importance of targeting intracellular pathways and neurotransmitter systems in developing effective treatments for OCD and related neuropsychiatric disorders.

The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis

During growth, Bacillus subtilis differentiates into subpopulations of motile individuals and non-motile chains, associated with dispersal and biofilm formation, respectively. The two cell types are dictated by the activity of the alternative sigma factor SigD encoded as the penultimate gene of the 27-kb long fla/che flagellar operon. The frequency of SigD-ON motile cells is increased by the heteromeric transcription factor SwrA·DegU that activates the fla/che promoter. Conversely, the frequency of motile cells is decreased by the heteromeric transcription factor SinR·SlrR, but the mechanism and location of inhibition is poorly understood. Here, using ChIP-Seq analysis, we determine the binding sites of the SinR·SlrR heteromer on the genome. We identified two sites within the fla/che operon that were necessary and sufficient to attenuate transcript abundance by causing premature termination upstream of the gene that encodes SigD. Thus, cell motility and the transition to biofilm formation depend on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle. More broadly, our study serves as a model for transcription factors that control transcriptional elongation and the regulation of long operons in bacteria.

Engineered promoter-free insulin-secreting cells provide closed-loop glycemic control

Diabetes mellitus is currently a priority health issue worldwide, but existing therapies suffer from insufficient donors, inability to provide glucose-dependent endogenous insulin secretion, transplantation risks, and immune rejection. Especially, reported engineered cells are mostly promoter-induced glucose-independent insulin producing cells. Here we constructed a closed-loop of insulin secretion with glucose-dependent IRES to achieve glucose-sensitive endogenous insulin secretion. Those cells successfully reversed hyperglycemia in diabetic mice for at least 60 days after transplantation without any significant immune rejection, demonstrating that our constructed engineered cellular grafts have good biocompatibility. Our findings hold great promise in the field of diabetes treatment and provide a new, glucose-dependent genetic engineering approach to insulin production, which is expected to solve many of the current problems faced in the clinical treatment of diabetes mellitus.

Pharmacological modulation of cellular senescence: Implications for breast cancer progression and therapeutic strategies

Senescence, defined by the cessation of cell proliferation, plays a critical and multifaceted role in breast cancer progression and treatment. Senescent cells produce senescence-associated secretory phenotypes (SASP) comprising inflammatory cytokines, chemokines, and small molecules, which actively shape the tumor microenvironment, influencing cancer development, progression, and metastasis. This review provides a comprehensive analysis of the types and origins of senescent cells in breast cancer, alongside their markers and detection methods. Special focus is placed on pharmacological strategies targeting senescence, including drugs that induce or inhibit senescence, their molecular mechanisms, and their roles in therapeutic outcomes when combined with chemotherapy and radiotherapy. By exploring these pharmacological interventions and their impact on breast cancer treatment, this review underscores the potential of senescence-targeting therapies to revolutionize breast cancer management.

Engaging an engineered PARP-2 catalytic domain mutant to solve the complex structures harboring approved drugs for structure analyses

The PARP-1/2 inhibitors have been approved for the treatment of cancers by modulating the enzymatic activity and/or the trapping ability for damaged DNA of PARP-1 and/or PARP-2, and the selective PARP-1 inhibitors are now attracting considerable attention with an aim to search for drug candidates with an improved safety. Exploring the structural basis of the selectivity and trapping capability of known PARP-1/2 inhibitors would be beneficial for the discovery of the improved inhibitors. Herein, a mutated PARP-2 catalytic domain, designated as catPARP-2SE, was engineered. It could be expressed in an elevated level and had capability to crystalize at 25 °C, which greatly facilitated obtaining PARP-2 crystals. Consequently, the complex structures of Fluzoparib, Pamiparib, Rucaparib, and Niraparib within PARP-2 were achieved. Taking advantage of these complexed structures, the detailed and quantitative analyses of protein-ligand and intra-protein interactions (αB-αF, αJ-αB, αJ-αF, ASL-αD and ASL-αF interfaces) were conducted with quantum chemistry methods (GFN2-xTB and IGMH). It suggested that the residues adjacent to Asp766 in the HD and ASL domains and the αJ-αF and ASL-αD interfaces were closely related to the selectivity and trapping mechanism. These results would provide some insights for the design and development of novel PARP-1/2 inhibitors with improved pharmacodynamic properties.

A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin

In recent years, a wealth of evidence revealed that many transcription-related molecules concentrate in membrane less nuclear compartments which are now recognized as relevant for transcription regulation. However, many aspects of this relationship remain unclear partly due to the experimental challenges of manipulating the distribution of transcription factors (TFs) in a controlled fashion. Here, we introduce a simple procedure to generate in live cells light-induced clusters (LICs) of TFs labeled with Janelia Fluor® probes through the HaloTag. When irradiated with the appropriate laser, the photooxidation/photobleaching of fluorescent molecules leads to the formation of a cluster which grows by incorporating other TF molecules, some through weak interactions. While the method was mostly tested with OCT4, other TFs such as SOX2 and the hormone-stimulated glucocorticoid receptor also form LICs. Relevantly, the inactive receptor in stem cells fails to form LICs suggesting that the process requires certain TF conformations and/or cellular contexts. Finally, we show that the recruitment of OCT4 to large LICs lowers its nucleoplasmic concentration and modifies both the overall distribution of the TF and its interactions with chromatin. In contrast, the generation of smaller LICs triggers the dissolution of nearby natural condensates of OCT4 but does not affect its nucleoplasmic concentration and OCT4-chromatin interactions. These results suggest that OCT4 condensates act as reservoirs, buffering variations in the nucleoplasmic concentration of this TF. This new method could be a valuable tool for exploring the relation between TFs distribution, landscape of interactions with chromatin and transcriptional output.

Progressive hippocampal senescence and persistent memory deficits in traumatic brain Injury: A role of delayed testosterone

Cellular senescence is a stable, pro-inflammatory cell cycle arrest that has been recently implicated in the persistent memory deficits experienced with repetitive mild traumatic brain injury (rmTBI). Testosterone (T) treatment immediately following traumatic brain injury (TBI) mitigates cognitive deficits and cellular dysfunction known to induce cellular senescence. However, it has yet to be elucidated whether the therapeutic window for T treatment can be extended to a subacute time post-injury. This study examined the progression of hippocampal cellular senescence after rmTBI and evaluated the effects of subacute T on persistent memory deficits and cellular senescence post-injury. Changes in senescence-associated markers in the hippocampus were quantified at 5- and 9-weeks post-injury (WPI). An age-independent progressive increase in senescence-associated gene expression was observed for Cdkn2a, Cdkn1a, and p53 protein levels, along with a decrease in Sirt1 gene expression. Acute and persistent cognitive deficits were observed in the rmTBI rats as compared to sham rats. Serum T levels were significantly decreased at 4 WPI. Testosterone administration at 5 WPI ameliorated these persistent memory deficits. Moreover, subacute T treatment reduced rmTBI-induced levels of Cdkn2a 4 weeks post-treatment. This study indicates that rmTBI results in a progressive cellular senescence pathology that may contribute to the underlying mechanisms of persistent cognitive symptoms. Therapeutically targeting cellular senescence within this extended temporal window holds implications for patients dealing with the chronic cognitive ramifications of rmTBI.

Characterization of intact mRNA-based therapeutics by charge detection mass spectrometry and mass photometry

The impressive success of mRNA-based vaccines to combat COVID-19 has encouraged biopharmaceutical companies to invest in broader applications of alike vaccines for various diseases. Analytical approaches must keep pace to support this surge in the development of mRNA-based therapies. Intact mass analysis of mid- to large mRNA molecules (>1,000 nt) poses significant analytical challenges due to mRNA size, heterogeneity, and instability. Here, we demonstrate how single-particle Orbitrap-based charge detection mass spectrometry (CDMS) and mass photometry (MP) approaches can rapidly measure the mass of various intact high-mass capped mRNAs, up to 9,400 nt (∼3 MDa) in size. While ensemble MS yielded approximate masses for mRNAs <2,000 nt, it failed to provide information on samples of longer sequences. The drawbacks of ensemble MS could be avoided by recording individual ions. Low-charge mRNA components showed unstable ion behavior, hampering initial CDMS measurements, whereas high-charge populations offered better signal-to-noise and reduced charge uncertainty, with drastically improved mass accuracy. Lastly, in-solution MP enabled the measurement of mRNAs with high accuracy, while revealing low amounts of mRNA fragments and dimers that are sometimes overlooked in CDMS. Overall, CDMS and MP provide complementary methods that enable the study of large heterogeneous mRNA without requiring prior digestion or online separation.

RNAa: Mechanisms, therapeutic potential, and clinical progress

RNA activation (RNAa), a gene regulatory mechanism mediated by small activating RNAs (saRNAs) and microRNAs (miRNAs), has significant implications for therapeutic applications. Unlike small interfering RNA (siRNA), which is known for gene silencing in RNA interference (RNAi), synthetic saRNAs can stably upregulate target gene expression at the transcriptional level through the assembly of the RNA-induced transcriptional activation (RITA) complex. Moreover, the dual functionality of endogenous miRNAs in RNAa (hereafter referred to as mi-RNAa) reveals their complex role in cellular processes and disease pathology. Emerging studies suggest saRNAs' potential as a novel therapeutic modality for diseases such as metabolic disorders, hearing loss, tumors, and Alzheimer's. Notably, MTL-CEBPA, the first saRNA drug candidate, shows promise in hepatocellular carcinoma treatment, while RAG-01 is being explored for non-muscle-invasive bladder cancer, highlighting clinical advancements in RNAa. This review synthesizes our current understanding of the mechanisms of RNAa and highlights recent advancements in the study of mi-RNAa and the therapeutic development of saRNAs.

TGFBI R124H mutant allele silencing in granular corneal dystrophy type 2 using topical siRNA delivery

In recent years, success has been achieved in treating several eye conditions with oligonucleotide-based therapies. Herein, we outline the experimentation involved in progressing selection and development of a lead therapeutic siRNA for R124H mutation of TGFBI gene which causes Granular Corneal Dystrophy Type 2 (GCD2/Avellino CD). Firstly, a series of siRNA designs, generated by a gene walk across the R124H TGFBI mutation site, were tested and a lead siRNA identified. The lead siRNA was delivered into an immortalised human corneal epithelial cell line to assess on-target efficacy and off-target effects. The in vivo efficacy of the lead R124H TGFBI siRNA, complexed with Bio-Courier technology, silicon stabilized hybrid lipid nanoparticles (sshLNP), was assessed in a mouse model of GCD2 which expressed the human R124H TGFBI transgene. Following topical siRNA application for 5 consecutive days, expression of the R124H mutant TGFBI transgene was measured and shown to be reduced by 22.4 % (± 15.7 %, p < 0.05). We investigated gene expression in the mouse cornea and showed expression of murine Tgfbi was 20-fold lower than TGFBI in human cornea, and expression of the mutant TGFBI transgene was a further 3-fold lower. This estimated 60-fold lower mutant transgene expression may explain the low frequency of corneal deposits observed in this mouse model, limiting its usefulness to test whether siRNA silencing is capable of phenotypic improvement or regression of GCD2/Avellino corneal dystrophy. We assessed WT TGFBI silencing in human primary corneal epithelial cells (PCEC) derived from human corneal limbal biopsy material, which express TGFBI at a similar level to human corneal biopsy. We demonstrated that a single 100 nM siRNA treatment, delivered by the sshLNP to the primary human corneal epithelial cells, gave 26.6 % (± 6.6 %, p < 0.001) reduction in TGFBI mRNA and a 15.4 % (±10.5 %, p < 0.05 %) reduction in TGFBi protein after 48 h. In consideration of the mutant gene expression levels in existing models of GCD2 disease, an ex vivo model of mutation-expressing primary corneal epithelial cells generated from corneal limbal biopsies from GCD2 patients would be more suitable than existing transgenic mouse models for future pre-clinical work in the development of gene silencing therapies for corneal dystrophies.

The interactions of Pu22 G-quadruplex, derived from c-MYC promoter sequence, with antitumor acridine derivatives-An NMR/MD combined study

Unsymmetrical bisacridines (UAs) represent a novel class of anticancer agents that exhibit significant antitumor activity against a wide range of cancer cell lines and solid tumors in vivo. UAs consist of two different acridine-based ring systems, which are connected by an aminoalkyl linker. Recent studies have demonstrated that UAs can suppress the c-MYC protooncogene, which is overexpressed in many tumor types. As a proposed molecular basis for this activity, UAs have been suggested to stabilize the G-quadruplex structure formed within the promoter region of c-MYC. In this study, we performed spectroscopic and computational analyses to investigate the stereochemistry of the c-MYC NHE III1 representative G-quadruplex, codenamed Pu22, in complex with two promising bisacridines, C-2045 and C-2053, as well as their monomeric counterparts, C-1311 and C-1748. C-1311 formed a well-defined 1:2 mol/mol DNA:ligand non-covalent adduct, whose solution structure was determined via 2D NMR. In contrast, C-1748 displayed weak and nonspecific interactions with the Pu22 G-quadruplex. Finally, the Pu22:UA complexes were examined using a combination of NMR and molecular modeling approaches, including umbrella sampling simulations. These results provide insights into the interaction mechanisms of UAs with G-quadruplex structures and highlight their potential as therapeutic agents targeting c-MYC.

Current strategies for senescence treatment: Focused on theranostic performance of nanomaterials

Age-related diseases imposed heavy burdens to the healthcare systems globally, while cell senescence served as one fundamental molecular/cellular basis for these diseases. How to tackle the senescence-relevant problems is a hotspot for biomedical research. In this review article, the hallmarks and molecular pathways of cell senescence were firstly discussed, followed by the introduction of the current anti-senescence strategies, including senolytics and senomorphics. With suitable physical or chemical properties, multiple types of nanomaterials were used successfully in senescence therapeutics, as well as senescence detection. Based on the accumulating knowledges for senescence, the rules of how to use these nanoplatforms more efficiently against senescence were also summarized, including but not limited to surface modification, material-cargo interactions, factor responsiveness etc. The comparison of these "senescence-selective" nanoplatforms to other treatment options (prodrugs, ADCs, PROTACs, CART etc.) was also given. Learning from the past, nanotechnology can add more choice for treating age-related diseases, and provide more (diagnostic) information to further our understanding of senescence process.

SHMT2 is essential for mammalian preimplantation embryonic development through de novo biosynthesis of nucleotide metabolites

Assisted reproductive technology (ART) is used widely and efficiently to treat infertility. During the ART procedure, one of the main factors affecting the success rate is abnormal development of preimplantation embryos. The establishment and maintenance of developmental competence are precisely regulated at different levels, while minor errors at early stages may result in adverse outcomes, including developmental arrest and implantation failure. As one of the major inputs, the regulatory mechanisms of metabolites in embryonic development are less known. In this study, we investigated the functional relevance of the metabolic enzyme serine hydroxymethyltransferase 2 (SHMT2) and deoxyribonucleotide (dNTP) metabolites in mouse preimplantation embryonic development. By using a well-characterized SHMT2 inhibitor, SHMT-IN-2, we effectively inhibited the catalytic activity of the SHMT2 enzyme, which led to developmental arrest at the pronuclear stage of the embryo. A low-input liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and applied for detecting dNTP content in embryos. We found that SHMT2 inhibition led to an insufficient dTTP supply and replication stress during the first mitotic cleavage, thereby causing failure of pronuclear fusion and developmental arrest. Our findings demonstrate a specific mechanism where, apart from building blocks of DNA, the availability of dNTPs contributes to the control of mouse preimplantation embryonic development.

FUBP3 enhances HIV-1 transcriptional activity and regulates immune response pathways in T cells

Far-upstream element-binding protein 3 (FUBP3) was identified at actively transcribing HIV promoters through chromatin affinity purification and mass spectrometry. Known for regulating cellular processes such as transcription and translation by binding to DNAs and RNAs, FUBP3's role in HIV transcriptional regulation was previously unrecognized. This study reveals that FUBP3 enhances HIV-1 transcriptional activation by interacting with Tat and trans-activation response (TAR)-RNA, critical for boosting viral transcription through recruitment of activating factors that promote RNA polymerase II (RNAPII) elongation. Transcriptomic analysis, chromatin immunoprecipitation, and biochemical assays demonstrated that FUBP3 associates with and stabilizes TAR-RNA, in a Tat-dependent manner, and enhances Tat steady-state levels via interaction with Tat's basic domain. Suppressing FUBP3 decreased HIV-1 transcription and altered expression of host genes linked to T cell activation and inflammation, underscoring its broad regulatory impact. Additionally, FUBP3 was enriched at active promoters, confirming its role in transcriptional regulation at specific genomic locations. These findings highlight FUBP3's critical role in the HIV-1 life cycle and suggest its potential as a therapeutic target in HIV-1 infection. Additionally, this study expands our understanding of FUBP3's functions in oncogenic and inflammatory pathways.

Hybrid micellar preparations for co-delivery of PARP-1 siRNA and quercetin for cataract treatment

Cataract remains a major cause of ocular blindness. Cyclic Arg-Gly-Asp-d-Phe-Lys (RGD) peptide was introduced to the surface of self-assembled hybrid micelles for the co-delivery of poly (ADP-ribose) polymerase 1 (PARP-1) small-interfering RNA (siRNA) and quercetin (Q/siP-c-M). Q/siP-c-M exhibited uniform particle size distribution, good dispersibility, high encapsulation efficiency, and strong stability for siRNA and quercetin. Q/siP-c-M significantly improved the transcorneal co-delivery of siRNA and quercetin to the deeper cornea and led to greater drug accumulation. In addition, Q/siP-c-M significantly increased the activity of catalase and the content of adenosine triphosphate (ATP), reduced the expression of PARP-1 protein, and effectively prevented lipid peroxidation in the lens. Among selenite-induced cataract rats, the Q/siP-c-M-treated rats produced higher levels of ATP and catalase, as well as lower levels of malondialdehyde and PARP-1 protein expression compared with those in the model group. Administration of quercetin further resulted in a decrease in neutrophil extracellular trap formation and downregulation of gene expression of related proteins and pro-inflammatory cytokines. These observations indicated that quercetin has the potential to serve as a therapeutic for alleviating an excessive inflammatory reaction characterized by an overabundance of neutrophil extracellular traps in the eyes. Therefore, this study highlights the potential of Q/siP-c-M against cataract development through the regulation of the immune response by regulating inflammatory conditions. Furthermore, Q/siP-c-M may offer benefits in terms of apoptosis attenuation for lens epithelial cells.

Correcting tau isoform ratios with a long-acting antisense oligonucleotide alleviates 4R-tauopathy phenotypes

Tau, a microtubule-binding protein linked to tauopathies like Alzheimer's disease and frontotemporal lobar degeneration (FTLD), has 3-repeat (3R) and 4-repeat (4R) isoforms. Accumulation of the 4R-tau is associated with FTLD, progressive supranuclear palsy (PSP), and cortico-basal degeneration (CBD). We previously showed that a loss of fused in sarcoma (FUS) or splicing factor, proline- and glutamine-rich (SFPQ) promoted 4R-tau accumulation, which induced FTLD-like behaviors and neurodegeneration in mice. Here, we developed antisense oligonucleotides (ASOs) modified with 2'-O, 4'-C-ethylene-bridged nucleic acids (ENAs), reducing the 4R-tau/3R-tau ratio while maintaining total tau expression from the MAPT gene. In vitro screening identified EN-06 as the most effective ENA. Intracerebroventricular (ICV) administration of EN-06 corrected the 4R/3R-tau ratio in FUS-silenced humanized tau mice and human iPSC-derived neurons. This treatment ameliorated disease phenotypes, including aberrant behaviors, spine dysmorphology, and neurodegeneration. The half-life of EN-06 after a single ICV administration was approximately 6 months in the brain, with splicing correction effects that persisted for 2 years. The efficacy of EN-06 was higher than that of 2'-O-methoxyethyl (MOE)-modified ASO (MO-06). These findings highlight the potential of ENA-modified ASOs to reduce 4R-tau while preserving total MAPT expression, thus offering a safe and long-acting treatment for 4R-tau-associated tauopathies.

AAV-mediated GBA1 and GDNF rescue neurological defects in a murine model of neuronopathic Gaucher disease

Neuropathic Gaucher disease (nGD) is a life-threatening disease that progresses rapidly and is caused by a glucosylceramidase beta 1 (GBA1) mutation, which encodes the lysosomal hydrolase β-glucocerebrosidase (GCase). Nerve damage in nGD, associated with stunted growth and development, arises from the degeneration and death of nervous system cells, which is often irreversible. Approved therapies effectively reduce the substrate burden outside the central nervous system (CNS) through augmenting mutant enzyme activity with pharmacologic recombinant GCase or by inhibiting glucocerebroside synthesis. However, these therapies do not provide neuroprotection. In this study, we developed a novel double-gene therapy based on adeno-associated virus (AAV), AAV9-GBA1-GDNF, which stably expresses human GBA1 and glial derived neurotrophic factor (GDNF) over the long term. Pathological, molecular, and proteomic tests in the nGD model confirmed that the early stages of the disease are characterized by GBA1 deficiency, loss of neuronal function, and even neuronal death. After treatment with AAV9-GBA1-GDNF, the lifespan of nGD mice was extended, and weight, brain development, and motor ability were recovered. Additionally, GBA1 and GDNF additively prevented irreversible neuronal death by activating the AKT/GSK3β pathway. These findings offer potential therapeutic strategies for nGD and other neurodegenerative diseases associated with lysosomal dysfunction.

Whole-transcriptome sequencing in neural and non-neural tissues of a mouse model identifies miR-34a as a key regulator in SMA pathogenesis

Spinal muscular atrophy (SMA) is a severe neurodegenerative disorder caused by deficiency of survival of motor neuron (SMN). While significant progress has been made in SMA therapy by rescuing SMN expression, limited knowledge about SMN downstream genes has hindered the development of alternative therapies. Here, we conducted whole-transcriptome sequencing of spinal cord, heart, and liver tissues of a severe SMA mouse model at early postnatal ages to explore critical coding and non-coding RNAs (ncRNAs). A large number of differentially expressed RNAs (DE-RNAs) were obtained, including 2,771 mRNAs, 382 microRNAs (miRNAs), 1,633 long ncRNAs, and 1,519 circular RNAs. Through in-depth data mining, we unveiled deregulation of miR-34a in all tissues. Analysis of competitive endogenous RNA networks of DE-RNAs identified multiple novel targets of miR-34a including Spag5 mRNA, lncRNA00138536, and circRNA007386. Further in vitro studies using mouse myoblast and human cardiomyocyte cell lines showed that knockdown of SMN upregulated miR-34a-5p and overexpression of miR-34a-5p alone disrupted cell-cycle progression through regulating its targets, recapitulating gene expression patterns observed in cardiac tissue of SMA mice. Our results identified a critical miRNA involved in SMA pathology, which sheds insights into the molecular basis of widespread tissue abnormalities observed in severe forms of SMA.

Genetic and environmental factors contributing to anophthalmia and microphthalmia: Current understanding and future directions

Anophthalmia is defined as a complete absence of one eye or both the eyes, while microphthalmia represents the presence of a small eye within the orbit. The estimated birth prevalence for anophthalmia is approximately 3 per 100000 live births, and for microphthalmia, it is around 14 per 100000 live births. However, combined evidence suggests that the prevalence of these malformations could be as high as 30 per 100000 individuals. Microphthalmia is reported to occur in 3.2% to 11.2% of blind children. Anophthalmia and microphthalmia (A/M) are part of a phenotypic spectrum alongside ocular coloboma, hypothesized to share a common genetic basis. Both A/M can occur in isolation or as part of a syndrome. Their complex etiology involves chromosomal aberrations, monogenic inheritance pattern, and the contribution of environmental factors such as gestational-acquired infections, maternal vitamin A deficiency (VAD), exposure to X-rays, solvent misuse, and thalidomide exposure. A/M exhibit significant clinical and genetic heterogeneity with over 90 genes identified so far. Familial cases of A/M have a complex genetic basis, including all Mendelian modes of inheritance, i.e., autosomal dominant, recessive, and X-linked. Most cases arise sporadically due to de novo mutations. Examining gene expression during eye development and the effects of various environmental variables will help us better understand the phenotypic heterogeneity found in A/M, leading to more effective diagnosis and management strategies. The present review focuses on key genetic factors, developmental abnormalities, and environmental modifiers linked with A/M. It also emphasizes at potential research areas including multiomic methods and disease modeling with induced pluripotent stem cell technologies, which aim to create innovative treatment options.

p14ARF interacts with γ-H2AX and is involved in the DNA damage response

p14ARF(ARF) is a tumor suppressor and functionally related to p53. Emerging evidences suggest that ARF triggers DNA damage in a p53-independent manner. However, it remains to be determined how ARF is involved in DNA damage response. Here, we report that ARF is critical in regulating the formation of DNA damage induced γ-H2AX foci. ARF binds to H2AX through its N-terminal domains to promote the phosphorylation of H2AX. The localization of ARF to the site of DNA breaks facilitates the formation of γ-H2AX foci in response to DNA damage. The knocking down of ARF significantly reduced γ-H2AX production and the number of γ-H2AX foci, leading to increased sensitivity to doxorubicin-induced cell death. Together, we propose that ARF plays a crucial role in DNA damage response through its association with H2AX and regulating γ-H2AX formation.

Design, synthesis and biological evaluation of 3-amino-6-(2-hydroxyphenyl)pyridazin-4-aryl derivatives as SMARCA2/4 degraders

SMARCA2/4, a pair of mutually exclusive core catalytic subunits of the chromatin remodeling complex SWI/SNF, play essential roles in regulating gene transcription. Given the pivotal role of SMARCA2/4 in sustaining the oncogenic transcription program and promoting proliferation in acute myeloid leukemia (AML), the development of non-selective degraders holds practical therapeutic implications. Herein, we designed and synthesized a series of proteolysis-targeting chimeras (PROTACs) by conjugating the VHL ligand to a SMARCA2/4 bromodomain ligand, 2-(6-amino-5-phenylpyridazin-3-yl)phenol, using various linkers. Preliminary evaluations identified A11 as the most potent molecule that efficiently degraded SMRACA2 (DC50 = 3.0 nM, Dmax = 98 %) and SMARCA4 (DC50 = 4.0 nM, Dmax = 98 %). A11 significantly inhibited the proliferation of hematological cancer cell lines, including MV-4-11, MOLM-13 and SU-DHL-4. It decreased the levels of SMARCA2/4 through the ubiquitin-proteasome system. Global proteome analysis revealed that A11 was able to selectively target and degrade SMARCA2/4. Additionally, A11 caused cell cycle arrest at the G0/G1 phase and induced cell apoptosis in MV-4-11 and MOLM-13 cells. It also blocked the oncogenic activity of MYC and other disease-related genes in AML cells. Overall, our data clarified that A11 is a promising SMARCA2/4 degrader for cancer therapy, which is worthy of further evaluation.

Maternal per- and polyfluoroalkyl substance concentrations and placental DNA methylation of thyroid hormone-related genes

Studies suggested that per- and polyfluoroalkyl substances (PFAS) may have adverse effects on fetus by altering placental DNA methylation. In the study, we explored associations of maternal PFAS concentrations with placental DNA methylation of thyroid hormone (TH)-related genes and the potential mediating role of DNA methylation levels in PFAS-fetal TH associations. We measured PFAS concentrations in maternal plasma in early pregnancy and levels of total triiodothyronine (TT3), total thyroxine (TT4), free triiodothyronine (FT3), free thyroxine (FT4), and thyroid stimulating hormone (TSH) in cord plasma. We assessed DNA methylation in 345 placental samples for five TH-related genes, i.e., iodothyronine deiodinase 3 (DIO3), solute carrier family 16 member 2 (SLC16A2), solute carrier organic anion transporter family member 1C1 (SLCO1C1), thyrotropin-releasing hormone (TRH), and transthyretin (TTR). We found the associations of PFDA with increased SLC16A2 methylation, PFOA with decreased SLCO1C1 methylation, PFOS with increased TRH methylation, and PFDoA with decreased TRH methylation, and these associations showed sex-specific patterns. Mediation analyses suggested placental SLCO1C1 and SLC16A2 methylation as potential mediators in the associations of PFOA with FT3 and PFUdA with TT4, respectively. These findings provided evidence for associations between prenatal PFAS exposure and epigenetic changes in placental TH-related genes.

Overview of M-LP/MPV17L, a novel atypical PDE and possible target for drug development

M-LP/Mpv17L (Mpv17-like protein) was initially identified as a novel protein during screening of age-dependently expressed genes in mouse kidney. Previous findings suggested that human Mpv17-like protein (M-LP/MPV17L) is involved in the maintenance of mitochondrial DNA (mtDNA), thus playing a role in cell defense against mitochondrial dysfunction, although its molecular mechanism of action has remained unknown. Recently, generation of M-LP/MPV17L-knockout (KO) cells using CRISPR-Cas9 technology has revealed that M-LP/MPV17L exerts cyclic nucleotide phosphodiesterase (PDE) activity despite lacking the conserved catalytic region and other structural motifs characteristic of the PDE family, and is one of the key components of pathways such as cAMP/cAMP-dependent protein kinase A (PKA) signaling. Moreover, generation of M-LP/Mpv17L-KO mice has revealed that deficiency of M-LP/Mpv17L results in development of β-cell hyperplasia and improved glucose tolerance, as well as physiological afferent cardiac hypertrophy. M-LP/MPV17L is a protein of great interest as it is a potential target for drug development. Therefore, in this review, we overview the molecular characteristics, regulation of expression, cellular functions, phenotypes detected in KO mice, and disease relevance of M-LP/MPV17L.