ASOptimizer: Optimizing antisense oligonucleotides through deep learning for IDO1 gene regulation.

Recent studies have highlighted the effectiveness of using antisense oligonucleotides (ASOs) for cellular RNA regulation, including targets that are considered undruggable; however, manually designing optimal ASO sequences can be labor intensive and time consuming, which potentially limits their broader application. To address this challenge, we introduce a platform, the ASOptimizer, a deep-learning-based framework that efficiently designs ASOs at a low cost. This platform not only selects the most efficient mRNA target sites but also optimizes the chemical modifications for enhanced performance. Indoleamine 2,3-dioxygenase 1 (IDO1) promotes cancer survival by depleting tryptophan and producing kynurenine, leading to immunosuppression through the aryl-hydrocarbon receptor (Ahr) pathway within the tumor microenvironment. We used ASOptimizer to identify ASOs that target IDO1 mRNA as potential cancer therapeutics. Our methodology consists of two stages: sequence engineering and chemical engineering. During the sequence-engineering stage, we optimized and predicted ASO sequences that could target IDO1 mRNA efficiently. In the chemical-engineering stage, we further refined these ASOs to enhance their inhibitory activity while reducing their potential cytotoxicity. In conclusion, our research demonstrates the potential of ASOptimizer for identifying ASOs with improved efficacy and safety.

The microRNA-485-3p concentration in salivary exosome-enriched extracellular vesicles is related to amyloid ß deposition in the brain of patients with Alzheimer's disease.

OBJECTIVES: Alzheimer's disease (AD) is an irreversible neurodegenerative disease characterized by progressive long-term memory loss and cognitive dysfunction. Neuroimaging tests for abnormal amyloid-ß (Aß) deposition are considered the most reliable methods for the diagnosis of AD; however, the cost for such testing is very high and generally not covered by national insurance systems. Accordingly, it is only recommended for individuals exhibiting clinical symptoms of AD supported by clinical cognitive assessments. Recently, it was suggested that dysregulated microRNA-485-3p (miRNA-485-3p) in the brain and cerebrospinal fluid is closely related to pathogenesis of AD. However, a relationship between circulating miRNA-485-3p in salivary exosome-enriched extracellular vesicles (EE-EV) and Aß deposition in the brain has not been observed. DESIGN & METHODS: Using quantitative real-time polymerase chain reaction, we analyzed miRNA-485-3p concentration in salivary EE-EV. We used receiver operating characteristic (ROC) curve analysis to evaluate its predictive value for Aß positron emission tomography (Aß-PET) positivity in patients with AD. RESULTS: Our results showed that the miRNA-485-3p concentration in salivary EE-EV isolated from patients with AD was significantly increased compared with that in the healthy controls (p < 0.0001). In the analysis of all participants, the miRNA-485-3p concentration was significantly increased in Aß-PET-positive participants compared to Aß-PET-negative participants (p < 0.0001). Further analysis using only AD patients also showed that the miRNA-485-3p concentration was significantly increased in Aß-PET-positive AD patients vs. Aß-PET-negative AD patients (p = 0.0063). The ROC curve analysis for differentiating Aß-PET-positive and negative participants showed that the area under the curve for miRNA-485-3p was 0.9217. CONCLUSION: These findings suggested that the miRNA-485-3p concentration in salivary EE-EV was closely related to Aß deposition in the brain and had high diagnostic accuracy for predicting Aß-PET positivity.

The role of microRNA-485 in neurodegenerative diseases.

Neurodegenerative diseases (NDDs) are age-related disorders characterized by progressive neurodegeneration and neuronal cell loss in the central nervous system. Neuropathological conditions such as the accumulation of misfolded proteins can cause neuroinflammation, apoptosis, and synaptic dysfunction in the brain, leading to the development of NDDs including Alzheimer's disease (AD) and Parkinson's disease (PD). MicroRNAs (miRNAs) are small noncoding RNA molecules that regulate gene expression post-transcriptionally via RNA interference. Recently, some studies have reported that some miRNAs play an important role in the development of NDDs by regulating target gene expression. MiRNA-485 (miR-485) is a highly conserved brain-enriched miRNA. Accumulating clinical reports suggest that dysregulated miR-485 may be involved in the pathogenesis of AD and PD. Emerging studies have also shown that miR-485 plays a novel role in the regulation of neuroinflammation, apoptosis, and synaptic function in the pathogenesis of NDDs. In this review, we introduce the biological characteristics of miR-485, provide clinical evidence of the dysregulated miR-485 in NDDs, novel roles of miR-485 in neuropathological events, and discuss the potential of targeting miR-485 as a diagnostic and therapeutic marker for NDDs.

Correction: Koh et al. Targeting MicroRNA-485-3p Blocks Alzheimer's Disease Progression. Int. J. Mol. Sci. 2021, 22, 13136.

The authors wish to make the following corrections to this paper [...].

Targeting MicroRNA-485-3p Blocks Alzheimer's Disease Progression.

Alzheimer's disease (AD) is a form of dementia characterized by progressive memory decline and cognitive dysfunction. With only one FDA-approved therapy, effective treatment strategies for AD are urgently needed. In this study, we found that microRNA-485-3p (miR-485-3p) was overexpressed in the brain tissues, cerebrospinal fluid, and plasma of patients with AD, and its antisense oligonucleotide (ASO) reduced Aß plaque accumulation, tau pathology development, neuroinflammation, and cognitive decline in a transgenic mouse model of AD. Mechanistically, miR-485-3p ASO enhanced Aß clearance via CD36-mediated phagocytosis of Aß in vitro and in vivo. Furthermore, miR-485-3p ASO administration reduced apoptosis, thereby effectively decreasing truncated tau levels. Moreover, miR-485-3p ASO treatment reduced secretion of proinflammatory cytokines, including IL-1ß and TNF-α, and eventually relieved cognitive impairment. Collectively, our findings suggest that miR-485-3p is a useful biomarker of the inflammatory pathophysiology of AD and that miR-485-3p ASO represents a potential therapeutic candidate for managing AD pathology and cognitive decline.

miRNAs as Therapeutic Tools in Alzheimer's Disease.

Alzheimer's disease (AD), an age-dependent, progressive neurodegenerative disorder, is the most common type of dementia, accounting for 50-70% of all dementia cases. Due to the increasing incidence and corresponding socioeconomic burden of dementia, it has rapidly emerged as a challenge to public health worldwide. The characteristics of AD include the development of extracellular amyloid-beta plaques and intracellular neurofibrillary tangles, vascular changes, neuronal inflammation, and progressive brain atrophy. However, the complexity of the biology of AD has hindered progress in elucidating the underlying pathophysiological mechanisms of AD, and the development of effective treatments. MicroRNAs (miRNAs, which are endogenous, noncoding RNAs of approximately 22 nucleotides that function as posttranscriptional regulators of various genes) are attracting attention as powerful tools for studying the mechanisms of diseases, as they are involved in several biological processes and diseases, including AD. AD is a multifactorial disease, and several reports have suggested that miRNAs play an important role in the pathological processes of AD. In this review, the basic biology of miRNAs is described, and the function and physiology of miRNAs in the pathological processes of AD are highlighted. In addition, the limitations of current pharmaceutical therapies for the treatment of AD and the development of miRNA-based next-generation therapies are discussed.

Innate Immunity and Cell Death in Alzheimer's Disease.

The innate immune system plays key roles in controlling Alzheimer's disease (AD), while secreting cytokines to eliminate pathogens and regulating brain homeostasis. Recent research in the field of AD has shown that the innate immune-sensing ability of pattern recognition receptors on brain-resident macrophages, known as microglia, initiates neuroinflammation, Aß accumulation, neuronal loss, and memory decline in patients with AD. Advancements in understanding the role of innate immunity in AD have laid a strong foundation to elucidate AD pathology and devise therapeutic strategies for AD in the future. In this review, we highlight the present understanding of innate immune responses, inflammasome activation, inflammatory cell death pathways, and cytokine secretion in AD. We also discuss how the AD pathology influences these biological processes.

Influenza Viruses: Innate Immunity and mRNA Vaccines.

The innate immune system represents the first line of defense against influenza viruses, which cause severe inflammation of the respiratory tract and are responsible for more than 650,000 deaths annually worldwide. mRNA vaccines are promising alternatives to traditional vaccine approaches due to their safe dosing, low-cost manufacturing, rapid development capability, and high efficacy. In this review, we provide our current understanding of the innate immune response that uses pattern recognition receptors to detect and respond to mRNA vaccination. We also provide an overview of mRNA vaccines, and discuss the future directions and challenges in advancing this promising therapeutic approach.

Diagnostic and therapeutic biomarkers for Alzheimer's disease in human-derived platelets.

BACKGROUND: Diagnosis of current Alzheimer's disease (AD) is difficult even for medical specialists, and there is no clear biomarker. Also, aging is highly related to the onset of AD. OBJECTIVES: The purpose of this study is to screen miRNA as an aging-considered biomarker for AD treatment and diagnosis. METHODS: The patient group for this study was divided into a young normal, old normal, or AD group. We developed a method of discovering sequentially expressed miRNAs to distinguish miRNAs that were sequentially expressed in the three groups. RESULTS: Sequentially expressed miRNAs correlated highly with the patient's age, and most showed expression patterns that distinguished young, old, and AD. Specifically, the miRNA expression we found showed similar patterns in the brains of patients with AD. Among the selected miRNAs, one set derived from the same precursor: The expression of miR-150 was a disease- and age-specific downregulation in both 3p and 5p forms, and the precursor also had the same pattern. We named that triple matching. Also, the found miR-150 precursor had AD-specific miRNA-imbalance characteristics. CONCLUSIONS: We developed a novel AD diagnostic method using triple matching and miRNA-imbalance. The triple matching and miRNA imbalance-based relative ratio diagnosis method we developed will be very powerful in resolving the challenges of absolute diagnostic quantification based on biomarker expression. Also, our research results suggest the possibility of a treatment target for AD.

The anti-inflammatory and anti-apoptotic effects of advanced anti-inflammation composition (AAIC) in heat shock-induced human HaCaT keratinocytes.

BACKGROUND: The development of natural cosmetic materials without side effects to protect skin from heat shock is necessary. We recently reported that advanced cooling composition (ACC) has anti-inflammatory effect in RAW 264.7 cells stimulated with lipopolysaccharide (LPS) and strong anti-microbial effect against Pseudomonas aeruginosa, Staphylococcus aureus, MRSA (Methicillin-resistant Staphylococcus aureus), Candida albicans, and Streptococcus mutans. AIMS: To further investigate whether advanced anti-inflammation composition (AAIC), newly developed from existing ACC has beneficial effects in heat shock-induced immortalized human keratinocytes (HaCaT cells), HaCaT cells were pretreated with AAIC before heat shock treatment. METHODS: Cell viability for heat shock treatment and different concentrations of AAIC in HaCaT cells were assessed by MTT assay. Anti-oxidative activity of AAIC was measured using the DPPH assay. The protein expression in heat shock-induced HaCaT cells treated with AAIC was evaluated by immunofluorescence staining and western blot analysis. RESULTS: AAIC, which is effective at 100 µg/mL concentration, was nontoxic in HaCaT cells and had an anti-oxidative effect demonstrated by scavenging DPPH free radicals. AAIC treatment significantly attenuated the aberrant levels of pro-inflammatory and pro-apoptotic signaling molecules in heat shock-induced HaCaT cells compared with control cells. CONCLUSION: AAIC potentially includes effective anti-oxidative activity, anti-inflammatory, and anti-apoptotic properties against heat shock-induced keratinocytes, suggesting that it can be provided as a raw material for imparting skin health.

Onion (Allium cepa L.) peel extract has anti-platelet effects in rat platelets.

The effects of onion peel extract (OPE) in collagen (5 µg/mL)-stimulated washed rat platelet aggregation were investigated. OPE inhibited platelet aggregation via inhibition of aggregation-inducing molecules, intracellular Ca(2+) and thromboxane A2 (TXA2) by blocking cyclooxygenase-1 (COX-1) and TXA2 synthase (TXAS) activities in a dose-dependent manner. In addition, OPE elevated the formation of cyclic adenosine monophosphate (cAMP), aggregation-inhibiting molecule, but not cyclic guanosine monophosphate (cGMP). High performance liquid chromatography (HPLC) analysis of OPE revealed that OPE contains quercetin, one of the major flavonoids, which has anti-platelet effect. In conclusion, we suggest that OPE is an effective inhibitor of collagen-stimulated platelet aggregation in vitro. Therefore, it can be a promising and safe strategy for anti-cardiovascular diseases.

Inhibitory effects of epigallocatechin-3-gallate on microsomal cyclooxygenase-1 activity in platelets.

In this study, we investigated the effect of (-)-epigallocatechin-3-gallate (EGCG), a major component of green tea catechins from green tea leaves, on activities of cyclooxygenase (COX)-1 and thromboxane synthase (TXAS), thromboxane A2 (TXA2) production associated microsomal enzymes. EGCG inhibited COX-1 activity to 96.9%, and TXAS activity to 20% in platelet microsomal fraction having cytochrome c reductase (an endoplasmic reticulum marker enzyme) activity and expressing COX-1 (70 kDa) and TXAS (58 kDa) proteins. The inhibitory ratio of COX-1 to TXAS by EGCG was 4.8. These results mean that EGCG has a stronger selectivity in COX-1 inhibition than TXAS inhibition. In special, a nonsteroid anti-inflammatory drug aspirin, a COX-1 inhibitor, inhibited COX-1 activity by 11.3% at the same concentration (50 µM) as EGCG that inhibited COX-1 activity to 96.9% as compared with that of control. This suggests that EGCG has a stronger effect than that of aspirin on inhibition of COX-1 activity. Accordingly, we demonstrate that EGCG might be used as a crucial tool for a strong negative regulator of COX-1/TXA2 signaling pathway to inhibit thrombotic disease-associated platelet aggregation.

Inhibitory effects of total saponin from Korean red ginseng via vasodilator-stimulated phosphoprotein-Ser(157) phosphorylation on thrombin-induced platelet aggregation.

In this study, we have investigated the effects of total saponin from Korean red ginseng (TSKRG) on thrombin-induced platelet aggregation. TSKRG dose-dependently inhibited thrombin-induced platelet aggregation with IC50 value of about 81.1 µg/mL. In addition, TSKRG dose-dependently decreased thrombin-elevated the level of cytosolic-free Ca(2+) ([Ca(2+)]i), one of aggregation-inducing molecules. Of two Ca(2+)-antagonistic cyclic nucleotides as aggregation-inhibiting molecules, cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), TSKRG significantly dose-dependently elevated intracellular level of cAMP, but not cGMP. In addition, TSKRG dose-dependently inhibited thrombin-elevated adenosine triphosphate (ATP) release from platelets. These results suggest that the suppression of [Ca(2+)]i elevation, and of ATP release by TSKRG are associated with upregulation of cAMP. TSKRG elevated the phosphorylation of vasodilator-stimulated phosphoprotein (VASP)-Ser(157), a cAMP-dependent protein kinase (A-kinase) substrate, but not the phosphorylation of VASP-Ser(239), a cGMPdependent protein kinase substrate, in thrombin-activated platelets. We demonstrate that TSKRG involves in increase of cAMP level and subsequent elevation of VASP-Ser(157) phosphorylation through A-kinase activation to inhibit [Ca(2+)]i mobilization and ATP release in thrombin-induced platelet aggregation. These results strongly indicate that TSKRG is a beneficial herbal substance elevating cAMP level in thrombin-platelet interaction, which may result in preventing of platelet aggregation-mediated thrombotic diseases.

Two functional forms of ACRBP/sp32 are produced by pre-mRNA alternative splicing in the mouse.

ACRBP/sp32 is a binding protein specific for the precursor (pro-ACR) and intermediate forms of sperm serine protease ACR. In this study, we examined the expression pattern, localization, and possible role of mouse ACRBP in spermatogenic cells and epididymal sperm. Unlike other mammalian ACRBPs, two forms of Acrbp mRNA-wild-type Acrbp-W and variant Acrbp-V5 mRNAs-were generated by alternative splicing of Acrbp in the mouse. ACRBP-W was synthesized in pachytene spermatocytes and haploid spermatids and immediately processed into a mature protein, ACRBP-C, by removal of the N-terminal half. The intron 5-retaining splice variant mRNA produced a predominant form of ACRBP, ACRBP-V5, that was present in pachytene spermatocytes and round spermatids, but was absent in elongating spermatids. ACRBP-W and ACRBP-V5 were both colocalized with pro-ACR in the acrosomal granules of early round spermatids, whereas the sperm acrosome contained only ACRBP-C. Glutathione S-transferase pull-down assays revealed that ACRBP-V5 and ACRBP-C possess a different domain capable of binding each of two segments in the C-terminal region of pro-ACR. Moreover, autoactivation of pro-ACR was remarkably accelerated by the presence of ACRBP-C. These results suggest that ACRBP-V5 and ACRBP-C may function in the transport/packaging of pro-ACR into acrosomal granules during spermiogenesis and in the promotion of ACR release from the acrosome during acrosomal exocytosis, respectively.