From function to translation: Decoding genetic susceptibility to human diseases via artificial intelligence.

While genome-wide association studies (GWAS) have discovered thousands of disease-associated loci, molecular mechanisms for a considerable fraction of the loci remain to be explored. The logical next steps for post-GWAS are interpreting these genetic associations to understand disease etiology (GWAS functional studies) and translating this knowledge into clinical benefits for the patients (GWAS translational studies). Although various datasets and approaches using functional genomics have been developed to facilitate these studies, significant challenges remain due to data heterogeneity, multiplicity, and high dimensionality. To address these challenges, artificial intelligence (AI) technology has demonstrated considerable promise in decoding complex functional datasets and providing novel biological insights into GWAS findings. This perspective first describes the landmark progress driven by AI in interpreting and translating GWAS findings and then outlines specific challenges followed by actionable recommendations related to data availability, model optimization, and interpretation, as well as ethical concerns.

Methodological advances in necroptosis research: from challenges to solutions.

Necroptosis is currently attracting the attention of the scientific community for its broad implications in inflammatory diseases and cancer. However, detecting ongoing necroptosis in vivo under both experimental and clinical disease conditions remains challenging. The technical barrier lies in four aspects, namely tissue sampling, real-time in vivo monitoring, specific markers, and distinction between different types of cell death. In this review, we presented the latest methodological advances for in vivo necroptosis identification. The advances highlighted the multi-parameter flow cytometry, sA5-YFP tool, radiolabeled Annexin V/Duramycin, Gallium-68-labeled IRDye800CW contrast agent, and SMART platform in vivo. We also discussed the up-to-date research models in studying necroptosis, particularly the mice models for manipulating and monitoring necroptosis. Based on these recent advances, this review aims to provide some advice on current necroptosis techniques and approaches.

Examining MLKL phosphorylation to detect necroptosis in murine mammary tumors.

Necroptosis occurs predominantly in the center of late-stage tumors and necroptotic cells are dispersed and difficult to be detected by Western blotting of key markers without enrichment by microdissection. To overcome these obstacles, this protocol provides a detailed immunohistochemistry-oriented approach including the steps of tumor isolation from mouse mammary tumor models, necrotic region identification by H&E staining, and necroptosis detection through examining mixed lineage kinase domain-like protein (MLKL) phosphorylation. This protocol could be applied to other types of solid tumors. For complete details on the use and execution of this protocol, please refer to Baik et al. (2021).

Reciprocal Regulation between lncRNA ANRIL and p15 in Steroid-Induced Glaucoma.

Steroid-induced glaucoma (SIG) is the most common adverse steroid-related effect on the eyes. SIG patients can suffer from trabecular meshwork (TM) dysfunction, intraocular pressure (IOP) elevation, and irreversible vision loss. Previous studies have mainly focused on the role of extracellular matrix turnover in TM dysfunction; however, whether the cellular effects of TM cells are involved in the pathogenesis of SIG remains unclear. Here, we found that the induction of cellular senescence was associated with TM dysfunction, causing SIG in cultured cells and mouse models. Especially, we established the transcriptome landscape in the TM tissue of SIG mice via microarray screening and identified ANRIL as the most differentially expressed long non-coding RNA, with a 5.4-fold change. The expression level of ANRIL was closely related to ocular manifestations (IOP elevation, cup/disc ratio, and retinal nerve fiber layer thickness). Furthermore, p15, the molecular target of ANRIL, was significantly upregulated in SIG and was correlated with ocular manifestations in an opposite direction to ANRIL. The reciprocal regulation between ANRIL and p15 was validated using luciferase reporter assay. Through depletion in cultured cells and a mouse model, ANRIL/p15 signaling was confirmed in cellular senescence via cyclin-dependent kinase activity and, subsequently, by phosphorylation of the retinoblastoma protein. ANRIL depletion imitated the SIG phenotype, most importantly IOP elevation. ANRIL depletion-induced IOP elevation in mice can be effectively suppressed by p15 depletion. Analyses of the single-cell atlas and transcriptome dynamics of human TM tissue showed that ANRIL/p15 expression is spatially enriched in human TM cells and is correlated with TM dysfunction. Moreover, ANRIL is colocalized with a GWAS risk variant (rs944800) of glaucoma, suggesting its potential role underlying genetic susceptibility of glaucoma. Together, our findings suggested that steroid treatment promoted cellular senescence, which caused TM dysfunction, IOP elevation, and irreversible vision loss. Molecular therapy targeting the ANRIL/p15 signal exerted a protective effect against steroid treatment and shed new light on glaucoma management.

Necroptosis and tumor progression.

Necroptosis, a form of programmed necrotic cell death, is a gatekeeper of host defense against certain pathogen invasions. The deregulation of necroptosis is also a key factor of many inflammatory diseases. Recent studies have revealed an important role of necroptosis in tumorigenesis and metastasis and imply the potential of targeting necroptosis as a novel cancer therapy. While its molecular mechanism has been well studied, details of the regulation and function of necroptosis of tumor cells in tumorigenesis and metastasis only began to emerge recently, and we discuss these herein.

TET-dependent GDF7 hypomethylation impairs aqueous humor outflow and serves as a potential therapeutic target in glaucoma.

Glaucoma is the leading cause of irreversible vision loss, affecting more than 70 million individuals worldwide. Circulatory disturbances of aqueous humor (AH) have long been central pathological contributors to glaucomatous lesions. Thus, targeting the AH outflow is a promising approach to treat glaucoma. However, the epigenetic mechanisms initiating AH outflow disorders and the targeted treatments remain to be developed. Studying glaucoma patients, we identified GDF7 (growth differentiation factor 7) hypomethylation as a crucial event in the onset of AH outflow disorders. Regarding the underlying mechanism, the hypomethylated GDF7 promoter was responsible for the increased GDF7 production and secretion in primary open-angle glaucoma (POAG). Excessive GDF7 protein promoted trabecular meshwork (TM) fibrosis through bone morphogenetic protein receptor type 2 (BMPR2)/Smad signaling and upregulated pro-fibrotic genes, α-smooth muscle actin (α-SMA) and fibronectin (FN). GDF7 protein expression formed a positive feedback loop in glaucomatous TM (GTM). This positive feedback loop was dependent on the activated TET (ten-eleven translocation) enzyme, which kept the GDF7 promoter region hypomethylated. The phenotypic transition in TM fortified the AH outflow resistance, thus elevating the intraocular pressure (IOP) and attenuating the nerve fiber layer. This methylation-dependent mechanism is also confirmed by a machine-learning model in silico with a specificity of 84.38% and a sensitivity of 89.38%. In rhesus monkeys, we developed GDF7 neutralization therapy to inhibit TM fibrosis and consequent AH outflow resistance that contributes to glaucoma. The neutralization therapy achieved high-efficiency control of the IOP (from 21.3 ± 0.3 to 17.6 ± 0.2 mmHg), a three-fold improvement in the outflow facility (from 0.1 to 0.3 µL/min · mmHg), and protection of nerve fibers. This study provides new insights into the epigenetic mechanism of glaucoma and proposes an innovative GDF7 neutralization therapy as a promising intervention.

Laquinimod exerts anti-inflammatory and antiapoptotic effects in retinal ischemia/reperfusion injury.

Retinal ischemia/reperfusion (I/R) occurs in various vision disabled ocular diseases, involved in acute glaucoma, diabetic retinopathy, ischemic optic neuropathy, hypertensive retinopathy and retinal vascular occlusion. Laquinimod (LQ), a new type of immunosuppressant, has been reported to exert anti-inflammatory effects on autoimmune diseases. This research aims to investigate the protective effect of LQ on I/R damage by focusing on inhibiting dysregulated neuroinflammation and neuronal apoptosis. In our study, mice were treated with LQ after high intraocular pressure (IOP)-induced retinal I/R injury. The data showed that LQ significantly attenuated high IOP-induced retinal ganglion cell (RGC) death and inner plexiform layer (IPL) thinning and inhibited microglial activation. The results of qRT-PCR, flow cytometry and Luminex multiplex assays demonstrated the anti-inflammatory action of LQ in BV2 cells stimulated with lipopolysaccharide (LPS). In addition, primary RGC apoptosis induced by oxygen-glucose deprivation/reperfusion (OGD/R) was also directly suppressed by LQ. Importantly, LQ inhibited the expression of cleaved caspase-8 and the downstream NLRP3 inflammasome and IL-1ß. In conclusion, our findings offer the first evidence that LQ treatment prevents retinal I/R damage. Furthermore, LQ could directly inhibit RGC apoptosis. Caspase-8 activation and subsequent inflammation can also be suppressed by LQ, which suggests that LQ may act through inhibiting the caspase-8 pathway. This study demonstrates a new mechanism of LQ and provides beneficial preclinical data for the clinical application of LQ.

LncRNA H19 initiates microglial pyroptosis and neuronal death in retinal ischemia/reperfusion injury.

Ischemia-reperfusion (I/R) is a common pathology when the blood supply to an organ was disrupted and then restored. During the reperfusion process, inflammation and tissue injury were triggered, which were mediated by immunocytes and cytokines. However, the mechanisms initiating I/R-induced inflammation and driving immunocytes activation remained largely unknown. In this study, we identified long non-coding RNA (lncRNA)-H19 as the key onset of I/R-induced inflammation. We found that I/R increased lncRNA-H19 expression to significantly promote NLRP3/6 inflammasome imbalance and resulted in microglial pyroptosis, cytokines overproduction, and neuronal death. These damages were effectively inhibited by lncRNA-H19 knockout. Specifically, lncRNA-H19 functioned via sponging miR-21 to facilitate PDCD4 expression and formed a competing endogenous RNA network (ceRNET) in ischemic cascade. LncRNA H19/miR-21/PDCD4 ceRNET can directly regulate I/R-induced sterile inflammation and neuronal lesion in vivo. We thus propose that lncRNA-H19 is a previously unknown danger signals in the molecular and immunological pathways of I/R injury, and pharmacological approaches to inhibit H19 seem likely to become treatment modalities for patients in the near future based on these mechanistic findings.

Trimetazidine protects retinal ganglion cells from acute glaucoma via the Nrf2/Ho-1 pathway.

Acute glaucoma is one of the leading causes of irreversible vision impairment characterized by the rapid elevation of intraocular pressure (IOP) and consequent retinal ganglion cell (RGC) death. Oxidative stress and neuroinflammation have been considered critical for the pathogenesis of RGC death in acute glaucoma. Trimetazidine (TMZ), an anti-ischemic drug, possesses antioxidative and anti-inflammatory properties, contributing to its therapeutic potential in tissue damage. However, the role of TMZ in acute glaucoma and the underlying molecular mechanisms remain elusive. Here, we report that treatment with TMZ significantly attenuated retinal damage and RGC death in mice with acute glaucoma, with a significant decrease in reactive oxygen species (ROS) and inflammatory cytokine production in the retina. Furthermore, TMZ treatment directly decreased ROS production and rebalanced the intracellular redox state, thus contributing to the survival of RGCs in vitro TMZ treatment also reduced the production of inflammatory cytokines in vitro Mechanistically, the TMZ-mediated inhibition of apoptosis and inflammatory cytokine production in RGCs occurred via the regulation of the nuclear factor erythroid 2-related factor 2/heme oxygenase 1/caspase-8 pathway. Moreover, the TMZ-mediated neuroprotection in acute glaucoma was abrogated when an HO-1 inhibitor, SnPP, was used. Our findings identify potential mechanisms of RGC apoptosis and propose a novel therapeutic agent, TMZ, which exerts a precise neuroprotective effect against acute glaucoma.

microRNA-21a-5p/PDCD4 axis regulates mesenchymal stem cell-induced neuroprotection in acute glaucoma.

Mesenchymal stem cells (MSCs) have been demonstrated to have promising therapeutic benefits for a variety of neurological diseases; however, the underlying mechanisms are poorly understood. Here, we showed that intravitreal infusion of MSCs promoted retinal ganglion cell (RGC) survival in a mouse model of acute glaucoma, with significant inhibition of microglial activation, production of TNF-α, IL-1ß, and reactive oxygen species, as well as caspase-8 and caspase-3 activation. In vitro, MSCs inhibited both caspase-8-mediated RGC apoptosis and microglial activation, partly via the action of stanniocalcin 1 (STC1). Furthermore, we found that microRNA-21a-5p (miR-21) and its target, PDCD4, were essential for STC1 production and the neuroprotective property of MSCs in vitro and in vivo. Importantly, miR-21 overexpression or PDCD4 knockdown augmented MSC-mediated neuroprotective effects on acute glaucoma. These data highlight a previously unrecognized neuroprotective mechanism by which the miR-21/PDCD4 axis induces MSCs to secrete STC1 and other factors that exert neuroprotective effects. Therefore, modulating the miR-21/PDCD4 axis might be a promising strategy for clinical treatment of acute glaucoma and other neurological diseases.

Precise long non-coding RNA modulation in visual maintenance and impairment.

Long non-coding RNAs (lncRNAs) are remarkably powerful, flexible and pervasive cellular regulators. With the help of cheaper RNA-seq, high-throughput screening of lncRNAs has become widely applied and has identified large numbers of specific lncRNAs in various physiological or pathological processes. Vision is known to be a complex and vital perception that comprises 80% of the sensory information we receive. A consensus has been reached that normal visual maintenance and impairment are primarily driven by gene regulation. Recently, it has become understood that lncRNAs are key regulators in most biological processes, including cell proliferation, apoptosis, differentiation, immune responses, oxidative stress and inflammation. Our review is intended to provide insight towards a comprehensive view of the precise modulation of lncRNAs in visual maintenance and impairment. We also highlight the challenges and future directions in conducting lncRNA studies, particularly in patients whose lncRNAs may hold expanded promise for diagnostic, prognostic and therapeutic applications.

The Role of Long Noncoding RNAs in Neurodegenerative Diseases.

Long noncoding RNAs (lncRNAs) are transcripts with low protein-coding potential but occupy a large part of transcriptional output. Their roles include regulating gene expression at the epigenetic, transcriptional, and post-transcriptional level in cellular homeostasis. However, lncRNA studies are still in their infancy and the functions of the vast majority of lncRNA transcripts remain unknown. It is generally known that the function of the human nervous system largely relies on the precise regulation of gene expression. Various studies have shown that lncRNAs have a significant impact on normal neural development and on the development and progression of neurodegenerative diseases. In this review, we focused on recent studies associated with lncRNAs in neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), multiple system atrophy (MSA), frontotemporal lobar degeneration (FTLD), and glaucoma. Glaucoma, caused by unexplained ganglion cell lesion and apoptosis, is now labeled as a chronic neurodegenerative disorder [1], and therefore, we discussed the association of lncRNAs with glaucoma as well. We illustrate the role of some specific lncRNAs, which may provide new insights into our understanding of the etiology and pathophysiology of the neurodegenerative diseases mentioned above.

Effects of renal sympathetic denervation on the atrial electrophysiology in dogs with pacing-induced heart failure.

BACKGROUND: Heart failure (HF) and atrial fibrillation (AF) are associated with sympathetic activation. Renal sympathetic denervation (RSD) can suppress AF vulnerability. The impact of RSD on atrial electrophysiology in experimental HF is unclear. METHODS: Twenty-two beagles were randomized into control, HF, and HF + RSD groups. Control dogs were implanted cardiac pacemakers without pacing. Dogs in the HF group underwent right ventricular pacing for 3 weeks at 240 beats/min to induce HF. The dogs in the HF + RSD group received RSD and underwent the same HF-inducing procedure. RESULTS: The P-wave dispersion was higher in HF dogs than in the control and HF + RSD dogs (19 ± 3.1 ms vs 13 ± 2.3 ms, 15 ± 2.9 ms, P = 0.04). Conduction time within the interatrium was significantly longer in the HF dogs than that in the control and HF + RSD dogs (39 ± 4 ms vs 31 ± 3 ms, 33 ± 4 ms; P = 0.03). Window of vulnerability (WOV) of AF was widened in the HF dogs than in the HF + RSD dogs (37 ± 5 ms vs 14 ± 3 ms; P < 0.01), while AF could not be induced (WOV = 0) in the control dogs during S1 S2 stimulation. The voltage in the threshold for AF inducibility was lower during ganglionated plexi stimulation in the HF dogs than in the control and HF + RSD dogs (1.8 ± 0.6 V vs 2.5 ± 0.6 V, 2.4 ± 0.4 V; P = 0.04). CONCLUSIONS: RSD could reverse the atrial electrical remodeling and decrease AF inducibility in dogs with pacing-induced HF.