Innovative gene delivery systems for retinal disease therapy

The human retina, a complex and highly specialized structure, includes multiple cell types that work synergistically to generate and transmit visual signals. However, genetic predisposition or age-related degeneration can lead to retinal damage that severely impairs vision or causes blindness. Treatment options for retinal diseases are limited, and there is an urgent need for innovative therapeutic strategies. Cell and gene therapies are promising because of the efficacy of delivery systems that transport therapeutic genes to targeted retinal cells. Gene delivery systems hold great promise for treating retinal diseases by enabling the targeted delivery of therapeutic genes to affected cells or by converting endogenous cells into functional ones to facilitate nerve regeneration, potentially restoring vision. This review focuses on two principal categories of gene delivery vectors used in the treatment of retinal diseases: viral and non-viral systems. Viral vectors, including lentiviruses and adeno-associated viruses, exploit the innate ability of viruses to infiltrate cells, which is followed by the introduction of therapeutic genetic material into target cells for gene correction. Lentiviruses can accommodate exogenous genes up to 8 kb in length, but their mechanism of integration into the host genome presents insertion mutation risks. Conversely, adeno-associated viruses are safer, as they exist as episomes in the nucleus, yet their limited packaging capacity constrains their application to a narrower spectrum of diseases, which necessitates the exploration of alternative delivery methods. In parallel, progress has also occurred in the development of novel non-viral delivery systems, particularly those based on liposomal technology. Manipulation of the ratios of hydrophilic and hydrophobic molecules within liposomes and the development of new lipid formulations have led to the creation of advanced non-viral vectors. These innovative systems include solid lipid nanoparticles, polymer nanoparticles, dendrimers, polymeric micelles, and polymeric nanoparticles. Compared with their viral counterparts, non-viral delivery systems offer markedly enhanced loading capacities that enable the direct delivery of nucleic acids, mRNA, or protein molecules into cells. This bypasses the need for DNA transcription and processing, which significantly enhances therapeutic efficiency. Nevertheless, the immunogenic potential and accumulation toxicity associated with non-viral particulate systems necessitates continued optimization to reduce adverse effects in vivo . This review explores the various delivery systems for retinal therapies and retinal nerve regeneration, and details the characteristics, advantages, limitations, and clinical applications of each vector type. By systematically outlining these factors, our goal is to guide the selection of the optimal delivery tool for a specific retinal disease, which will enhance treatment efficacy and improve patient outcomes while paving the way for more effective and targeted therapeutic interventions.

Investigation of epilepsy-related genes in a Drosophila model

Complex genetic architecture is the major cause of heterogeneity in epilepsy, which poses challenges for accurate diagnosis and precise treatment. A large number of epilepsy candidate genes have been identified from clinical studies, particularly with the widespread use of next-generation sequencing. Validating these candidate genes is emerging as a valuable yet challenging task. Drosophila serves as an ideal animal model for validating candidate genes associated with neurogenetic disorders such as epilepsy, due to its rapid reproduction rate, powerful genetic tools, and efficient use of ethological and electrophysiological assays. Here, we systematically summarize the advantageous techniques of the Drosophila model used to investigate epilepsy genes, including genetic tools for manipulating target gene expression, ethological assays for seizure-like behaviors, electrophysiological techniques, and functional imaging for recording neural activity. We then introduce several typical strategies for identifying epilepsy genes and provide new insights into gene‒gene interactions in epilepsy with polygenic causes. We summarize well-established precision medicine strategies for epilepsy and discuss prospective treatment options, including drug therapy and gene therapy for genetic epilepsy based on the Drosophila model. Finally, we also address genetic counseling and assisted reproductive technology as potential approaches for the prevention of genetic epilepsy.

Genome wide landscaping of copy number variations for horse inter-breed variability

Copy number variations (CNVs) have become widely acknowledged as a significant source of genomic variability and phenotypic variance. To understand the genetic variants in horses, CNVs from six Indian horse breeds, namely, Manipuri, Zanskari, Bhutia, Spiti, Kathiawari and Marwari were discovered using Axiom™ Equine Genotyping Array. These breeds differed in agro-climatic adaptation with distinct phenotypic characters. A total of 2668 autosomal CNVs and 381 CNV regions (CNVRs) were identified with PennCNV tool. DeepCNV was employed to re-validate to get 883 autosomal CNVs, of which 9.06% were singleton type. A total of 180 CNVRs were identified after DeepCNV filtering with the estimated length of 3.12 Kb-4.90 Mb. The functional analysis showed the majority of the CNVRs genes enriched for sensory perception and olfactory receptor activity. An Equine CNVs database, EqCNVdb (http://backlin.cabgrid.res.in/eqcnvdb/) was developed which catalogues detailed information on the horse CNVs, CNVRs and gene content within CNVRs. Also, three random CNVRs were validated with real-time polymerase chain reaction. These findings will aid in the understanding the horse genome and serve as a preliminary foundation for future CNV association research with commercially significant equine traits. The identification of CNVs and CNVRs would lead to better insights into genetic basis of important traits.

Causal relationship between chronic kidney disease, renal function, and venous thromboembolism: a bidirectional Mendelian randomization study

BACKGROUND

Chronic kidney disease (CKD) and impaired renal function have been implicated in venous thromboembolism (VTE), but their causal relationships remain uncertain. This study employs Mendelian randomization (MR) to elucidate the potential bidirectional causal effects between CKD, renal function biomarkers, and VTE.

METHODS

We collated datasets from genome-wide association studies conducted among European individuals to perform MR analyses. The primary method utilized was the random-effect inverse variance-weighted (IVW) approach, with MR-Egger and the weighted median approaches employed as supplemental techniques. Several sensitivity studies were performed to assess the findings' robustness.

RESULTS

We identified a link between elevated serum creatinine levels and both VTE (OR: 1.14, 95% CI: 1.05-1.24, p = 0.001) and PE (OR: 1.20, 95% CI: 1.08-1.33, p = 0.001). After outlier removal and Bonferroni correction, the Cr-VTE association lost significance (p = 0.005). A suggestive causal relationship was found between eGFR and VTE (OR: 0.38, 95% CI: 0.20-0.73, p = 0.004), DVT (OR: 0.37, 95% CI: 0.16-0.87, p = 0.022), and PE (OR: 0.29, 95% CI: 0.12-0.66, p = 0.004). No causal effects of CKD or BUN on VTE or its subtypes were observed. Reverse causality inferences did not reveal any meaningful results.

CONCLUSIONS

This MR analysis provides evidence that elevated serum creatinine is associated with a higher risk of VTE and PE, while reduced eGFR may be a potential risk factor for VTE and its subtypes. These findings highlight the need for proactive monitoring and preventive strategies in individuals with impaired renal function. Further studies are warranted to confirm these associations and explore underlying mechanisms.

Deciphering the role of APOE in cerebral amyloid angiopathy: from genetic insights to therapeutic horizons

Cerebral amyloid angiopathy (CAA), characterized by the deposition of amyloid-β (Aβ) peptides in the walls of medium and small vessels of the brain and leptomeninges, is a major cause of lobar hemorrhage in elderly individuals. Among the genetic risk factors for CAA that continue to be recognized, the apolipoprotein E (APOE) gene is the most significant and prevalent, as its variants have been implicated in more than half of all patients with CAA. While the presence of the APOE ε4 allele markedly increases the risk of CAA, the ε2 allele confers a protective effect relative to the common ε3 allele. These allelic variants encode three APOE isoforms that differ at two amino acid positions. The primary physiological role of APOE is to mediate lipid transport in the brain and periphery; however, it has also been shown to be involved in a wide array of biological functions, particularly those involving Aβ, in which it plays a known role in processing, production, aggregation, and clearance. The challenges posed by the reliance on postmortem histological analyses and the current absence of an effective intervention underscore the urgency for innovative APOE-targeted strategies for diagnosing CAA. This review not only deepens our understanding of the impact of APOE on the pathogenesis of CAA but can also help guide the exploration of targeted therapies, inspiring further research into the therapeutic potential of APOE.

Recent Progress in Omics Studies of Sleep and Circadian Phenotypes

Purpose of review

Sleep and circadian biology is fundamental to human health. Following the advancement in sleep medicine and availability of multi-omics technology, this review outlines the current knowledge regarding genetic basis and multi-omics research on circadian rhythm and the two most prevalent sleep disorders, obstructive sleep apnea (OSA) and insomnia.

Recent findings

Genome wide association analyses identified variants across circadian genes and genes pertinent to inflammation, obesity and neuronal function associated with OSA and insomnia. Multi-omics integration has led to novel breakthroughs in identifying systemic biomarkers and elucidating cascades, and causal associations underpinning these complex traits.

Summary

Multi-omics studies in sleep and circadian rhythm possess great potential in unveiling molecular mechanisms behind circadian rhythm and sleep, thereby advancing personalized medicine in the long term. Nevertheless, researchers should remain mindful of existing challenges in genetic and multi-omics sleep research, including data harmonization and existing racial and ethnic disparities in data collection and availability, limiting research generalizability.

Drug survival of omalizumab in atopic asthma: Impact of clinical and genetic variables

It is estimated that 40-50% of severe asthma has an atopic basis, representing a clinical challenge and a significant economic burden for healthcare systems. The most effective treatment has emerged with the use of biologic therapies such as omalizumab; however, the rate of therapy switching due to loss of efficacy is high, which has a negative impact on the healthcare system. The aim was to evaluate the influence of genetic polymorphisms as predictors of omalizumab survival. We conducted a retrospective observational cohort study of 110 patients with uncontrolled severe allergic asthma treated with omalizumab in a tertiary hospital. We analyzed FCER1A (rs2251746, rs2427837), FCER1B (rs1441586, rs573790, rs1054485, rs569108), C3 (rs2230199), FCGR2A (rs1801274), FCGR2B (rs3219018, rs1050501), FCGR3A (rs10127939, rs396991), IL1RL1 (rs1420101, rs17026974, rs1921622) and GATA2 (rs4857855) by real-time PCR using Taqman probes. Drug survival was defined as the time from initiation to discontinuation of omalizumab. Cox regression analysis adjusted for the presence of respiratory disease, GERD, SAHS and years with asthma showed that the SNPs FCER1B rs573790 - CT (p < .001; HR = 3.38; CI95% = 1.66-6.87), FCGR3A rs10127939-AC (p = .018; HR = 3.85; CI95% = 1.25-11.81) and FCGR3A rs396991-CC (p = .020; HR = 2.23; CI95% = 1.14-4.38) were the independent variables associated with worse survival in patients diagnosed with asthma. A trend toward statistical significance was also found between and FCGR3A rs10127939-CC (p = .080; HR = 0.13; CI95% = 0.01-1.28) and longer drug survival. The results of this study demonstrate the potential influence of the polymorphisms studied on omalizumab survival and the clinical benefit that could be achieved by defining predictive biomarkers of drug survival.

Relationship between the CUBN and the MIA3 gene copy number variation and growth traits in different cattle breeds

Copy number variations (CNV) are important genetic variations. The endogenous factors cobalamin receptor (CUBN) and MIA SH3 domain ER-derived factor 3 (MIA3) are associated with bone/muscle development and intramuscular fat deposition. There have been no reports on the effects of CUBN and MIA3 CNVs on growth traits of Chinese cattle. This study aimed to determine the correlation between the CUBN and MIA3 CNVs and growth traits in Chinese cattle. qRT-PCR was used to detect the distribution of CUBN and MIA3 CNV and the expression levels of their mRNA, and correlation analysis was conducted between CNV and growth traits. The CUBN was differentially expressed in different breeds of cattle, and CUBN CNV correlated significantly with body height, hip height, body slanting length, and hip width of Grassland Red cattle (CYH); eye muscle area of Yanbian cattle (YB) and Yan Yellow cattle (YH). MIA3 showed no CNV in CYH and YB cattle, and only one deletion type occurred in YH cattle. CUBN and MIA3 mRNA have different expression patterns in different cattle breeds and tissues. In conclusion, CUBN CNV is correlated significantly with growth traits in Chinese cattle and is a novel molecular marker that could be exploited in cattle breeding.

Zellweger syndrome; identification of mutations in PEX19 and PEX26 gene in Saudi families

BACKGROUND

Peroxisome biogenesis disorders (PBD) affect multiple organ systems. It is characterized by neurological dysfunction, hypotonia, ocular anomalies, craniofacial abnormalities, and absence of peroxisomes in fibroblasts. PBDs are associated with mutations in any of fourteen different PEX genes, which are involved in peroxisome biogenesis. Zellweger spectrum disorder (ZSD) is a severe form of PBD. More than 90% of the ZSD cases have mutations in PEX1, PEX6, PEX10, PEX12, and PEX26. Mutations in the PEX19 gene are rarely associated with PBD/ZSD; however, a large proportion of PEX26 mutations are associated with ZSD.

METHODS

We recruited two Saudi families with multiple affected individuals with dysmorphic features, including hypertelorism, large open fontanelles, generalized hypotonia, and epicanthal folds with poor reflexes since birth. Whole exome sequencing (WES) and Sanger sequencing was performed to identify the genetic cause. The frequency and pathogenicity of the identified mutations were assessed using various online bioinformatics tools.

RESULTS

WES identified a novel nonsense variant (c.367C > T) in the PEX19 gene in family A patients. This nonsense mutation was predicted to cause premature termination (p.Gln123*). A previously reported synonymous variant (c.228C > T; p.Gly76Gly) in PEX26 was found in a patient from family B. Both variants were segregating in an autosomal recessive manner in the respective families.

CONCLUSION

The present study has added a novel nonsense mutation to the mutation spectrum of PEX19, which is the second null mutation identified to date. Moreover, in this study, the importance of a synonymous exonic variant of PEX26 close to the splice donor site was explored in relation to pre-mRNA splicing and resulting disease manifestations.

A pilot study of apolipoprotein E genotype and associations with maternal lipid levels and small for gestational age outcomes in non-hypertensive pregnancies

OBJECTIVE

The aim of the present pilot study was to determine associations between maternal Apolipoprotein E (ApoE) genotype, lipid levels during pregnancy, fetal growth, and placental pathology.

METHODS

In this case-control study, serum samples from pregnant women without hypertension who delivered small-for-gestational age (SGA) infants (n = 50) were matched on gestational age at sample collection with non-SGA infants (n = 100). ApoE allele distributions and lipid levels were compared between cases and controls and among placental pathological findings.

RESULTS

No differences in ApoE genotypes were noted between groups. High density lipoprotein (HDL) cholesterol levels were higher in ε2 carriers versus ε3/ε3 and ε4 carriers (78.1 vs. 67.7 vs. 64.0 mg/dL, p < 0.01 and p < 0.001, respectively), and in SGA pregnancies (73.2 vs 65.1 mg/dL, p = 0.003).

CONCLUSION

Findings suggest increased HDL in pregnancy may be associated with the ε2 allele and decreased fetal growth. These findings provide a useful starting point for further research and should be explored in larger population-based studies.

Genetic variation in zona pellucida-3 (ZP3) gene and its association with litter size variation in Kari sheep

Variation in litter size (LS) in sheep is linked to genetic factors, including the Zona pellucida-3 (ZP3) gene, which plays a role in ovine reproductive processes. This study examined the association between ZP3 gene variations and LS in Kari sheep. Two groups of 160 Kari ewes were analysed: one consistently producing singletons and another producing twins, with occasional triplets. Additionally, Madakhlasht sheep, which sometimes produce twins, and Balkhi sheep, which produce only singletons, were used as references. The entire ZP3 gene was amplified using PCR and sequenced at 30× with Next Generation Sequencing. Bioinformatics analysis identified 70 variants across the three breeds, located in upstream regions, introns, and exons. Notably, two point mutations and a six-nucleotide insertion were found upstream of the initiation codon in twin-producing Kari ewes, potentially affecting ZP3 expression and LS. Two missense mutations (I101L in exon 1 and R408H in exon 8) were heterozygous in twin-producing Kari ewes but homozygous in other groups, correlating with LS. Protein modelling suggested that the I101L mutation alters the binding site, potentially impacting protein function. These findings indicate that ZP3 gene variations influence reproductive efficiency and LS in sheep, with specific variants serving as potential markers for selective breeding to enhance LS.

Unveiling the role of miRNAs in Diminished Ovarian Reserve: an in silico network approach

MicroRNAs (miRNAs) have acquired an increased recognition to unravel the complex molecular mechanisms underlying Diminished Ovarian Reserve (DOR), one of the main responsible for infertility. To investigate the impact of miRNA profiles in granulosa cells and follicular fluid, crucial players in follicle development, this study employed a computational network theory approach to reconstruct potential pathways regulated by miRNAs in granulosa cells and follicular fluid of women suffering from DOR. Available data from published research were collected to create the FGC_MiRNome_MC, a representation of miRNA target genes and their interactions. 365 hubs were identified within the network, representing potential key regulators, and 210 nodes that act as both hubs and bottlenecks (H&BN nodes), suggesting that they may control the information flow within the network. GO enrichment analysis of the 210 H&BN nodes revealed their involvement in fundamental cellular processes relevant to ovarian function. In particular, the cluster analysis identified several shared pathways between cluster 1 and cluster 2 involved in the RAS/MAPK pathway, which plays a critical role in cell proliferation, differentiation and survival. These findings suggest that miRNAs play a significant role in DOR and highlight the potential of the RAS/MAPK pathway as a target for further investigation. Additionally, the genes identified as both hubs and bottlenecks revealed interesting connections to reproductive health in KO mice models. This in silico approach provides valuable insights into potential biomarkers and therapeutic targets for age-related reproductive disorders.

A penny for your thoughts: three perspectives on financial problems and their associated factors of people with psychotic disorders

PURPOSE

Financial problems are of influence on mental health, and vice versa. Indeed, finances are a key challenge for people with psychosis. To gain deeper insights into these challenges, a qualitative approach focusing on all perspectives within the therapeutic triad is needed. This study aims to investigate perspectives of people with psychosis, family members and mental healthcare professionals on people with psychosis' financial problems, and associated factors.

METHODS

Fourteen people with psychosis, 15 family members and 16 professionals were recruited using purposive sampling, and participated in semi-structured, one-on-one interviews. Data was analysed using iterative thematic data-analysis.

RESULTS

Interviews revealed five themes of financial problems: Covering expenses, Financial performance, Living conditions and housing, Personal conflicts and victimization, and Regulations and legislation. Five themes were identified as factors associated with financial problems: Psychotic symptoms, Indirect factors related to psychosis, Substance use and addiction, Financial upbringing and life events, and Societal contextual factors.

DISCUSSION

People in the therapeutic triad largely mentioned similar, wide-ranging, and often co-occurring (factors associated with) financial problems of people with psychosis, risking vicious cycles. Fostering awareness and collaborative efforts among stakeholders is essential to breaking these cycles of financial problems for individuals with psychosis.

Sulfatase-mediated peroxidase-like activity: A chemiluminescence-based platform for high-throughput screening of natural inhibitors in cancer therapy

Sulfatase, traditionally known for its role in sulfate ester hydrolysis, has recently emerged as a potential player in tumor biology through its involvement in oxidative stress pathways. Here, we demonstrate for the first time that sulfatase exhibits peroxidase-like activity, catalyzing the generation of singlet oxygen (1O2) in the presence of oxygen. Based on the sulfatase-dependent 1O2 generation, the developed adamantly-enolether chemiluminescence probe QM-CF for imaging tumors of high sulfatase expression further verified the theory that sulfatase can be involved in tumor development. High-throughput screening (HTS) of natural compounds and clinical drugs identified scutellarin and sinomenine as potent sulfatase inhibitors that suppress tumor growth in mice. Mechanistic investigations revealed that these inhibitors modulate oxidative stress by downregulating MAPK and NF-κB pathways. Our findings unveil a previously unappreciated role of sulfatase in tumor-related oxidative stress and provide a promising platform for the discovery of novel sulfatase inhibitors, and advancing cancer therapeutics.

Mendelian randomization analysis identifies ERAP1 and IL23R as potential drug targets for ankylosing spondylitis

BACKGROUND

Ankylosing spondylitis (AS) is a chronic inflammatory disease primarily affecting the spine and pelvis, leading to ankylosis, stiffness, and reduced quality of life. Despite therapeutic advances, identifying novel drug targets remains critical.

METHODS

This Mendelian randomization (MR) study leveraged proteome-wide analysis, utilizing data from five genome-wide association studies (GWAS) for proteomics exposure. Outcome data included 3162 European ancestry cases and 294,770 controls from FinnGen R10, and replication analyses used two plasma proteomic datasets (ARIC: 4657 proteins in 7213 individuals; UK Biobank: 4907 proteins in 35,559 participants) and UK Biobank AS GWAS (1344 cases, 324,074 controls). Sensitivity analyses, including Bayesian co-localization and Steiger's direction test, were conducted to ensure robust findings. Protein-protein interaction (PPI) networks were constructed to explore interactions between identified proteins and known AS drug targets.

RESULTS

After FDR adjustment, circulating ERAP1 (OR = 1.30, 95 % CI: 1.21-1.39, P = 8.18 × 10-14) and IL23R (OR = 2.21, 95 % CI: 1.61-3.03, P = 9.47 × 10-7) were genetically linked to increased AS risk, while IL1RL2 showed a protective effect (OR = 0.70, 95 % CI: 0.58-0.85, P = 3.22 × 10-4). Steiger's test confirmed directionality (P < 1.70 × 10-15), and Bayesian co-localization supported shared causal variants (PPH4 > 0.75 for IL23R/IL1RL2). PPI networks revealed interactions between ERAP1, IL23R, and known AS targets. Replication validated ERAP1 and IL23R associations but not IL1RL2.

CONCLUSION

Genetically determined levels of ERAP1 and IL23R are robustly associated with AS risk, highlighting their potential as therapeutic targets. This study demonstrates the utility of MR in identifying drug targets for complex diseases, providing a foundation for further clinical investigation into their therapeutic potential.

Causal Links between Gut Microbiota, Blood Metabolites, Immune Cells, Inflammatory Proteins, and Myopia: A Mendelian Randomization Study

Purpose

This study aimed to investigate causal relationships between gut microbiota, blood metabolites, immune cell traits, circulating inflammatory proteins, and myopia through Mendelian randomization (MR) analysis.

Design

Mendelian randomization study.

Subjects

Genome-wide association study (GWAS) data of 412 gut microbiota, 1400 blood metabolites/metabolite ratios, 731 immune cell traits, and 91 circulating inflammatory proteins from the public GWAS database. Genome-wide association study data of myopia from the public GWAS database and FinnGen consortium.

Methods

Two-sample MR analysis and meta-analysis were employed using 4 methods, with inverse-variance weighted as the primary approach, to investigate potential causal links. Metabolic pathway analysis was conducted to explore metabolic pathways. The Cochran Q-test, MR-Egger intercept test, and MR-PRESSO were used for sensitivity analyses. Mediation and reverse MR analyses were also carried out to identify potential mediation relationships and modification effects of myopia.

Main Outcome Measures

Causal relationships between gut microbiota, blood metabolites, immune cell traits, circulating inflammatory proteins, and myopia.

Results

We identified causal effects of 34 and 22 gut microbiota/bacterial pathways, 131 and 98 blood metabolites/metabolite ratios, 60 and 37 immune cell traits, and 5 and 2 circulating inflammatory proteins on myopia (ukb-b-6353 and R10_H7_MYOPIA, respectively). Overlapping causal relationships were found for 1 gut bacterial pathway, 10 blood metabolites/metabolite ratios, and 2 immune cell traits across both outcomes; however, none of these overlaps reached significance after meta-analysis. The Small Molecule Pathway Database and Kyoto Encyclopedia of Genes and Genomes database enriched 14 significant pathways. Flavin adenine dinucleotide was involved in 8 pathways in both databases. Furthermore, the causal effect of glycochenodeoxycholate glucuronide on myopia was mediated by acetyl-CoA fermentation to butanoate lI, with mediation proportion of 19.03% (ukb-b-6353) and 19.48% (R10_H7_MYOPIA). Reverse MR analysis identified modification effects of myopia (ukb-b-6353) on gut microbiota, blood metabolites, and circulating inflammatory proteins.

Conclusions

These findings demonstrated significant causal relationships between gut microbiota, blood metabolites, immune cell traits, circulating inflammatory proteins, and myopia. Gut microbiota pathway may mediate the causal effects of blood metabolite on myopia. This may provide researchers with a new perspective in exploring the biological mechanisms of myopia and may lead to the exploration of earlier treatment strategies.

Financial Disclosures

The author(s) have no proprietary or commercial interest in any materials discussed in this article.

Conformational features of guinea pig apolipoprotein E offer insights into functioning of human apolipoprotein E

Apolipoprotein (apo) E is a major cholesterol transport protein in the plasma and brain of humans, with the APOE ε4 allele (coding for R112) associated with a higher risk for cardiovascular and Alzheimer's diseases (CVD and AD, respectively) compared to APOE ε3 (coding for C112). The molecular basis underlying the link between APOE ε4 and CVD/AD is poorly understood. Here apoE from Cavia porcellus (guinea pig, GP), which is 72 % identical to human apoE4 but lacking residues 193-197 and 246-252, a feature noted in all hystricomorph apoE, was used as a model to understand the role of apoE4. Western blot with anti-human apoE antibody revealed cross reactivity with bacterially expressed recombinant GP apoE. GP apoE solubilized phospholipids far more efficiently than apoE3/E4 but promoted macrophage cholesterol efflux to a similar extent. The overall secondary structure and tetrameric organization of GP apoE were broadly similar to those of apoE3/E4. Guanidine HCl-induced denaturation revealed a biphasic unfolding pattern indicative of a two-domain architecture for GP apoE. Hydrogen-deuterium exchange coupled to mass spectrometry of GP apoE revealed mixed EX1/EX2 kinetics similar to that noted for apoE4, with peak broadening indicative of the presence of partially folded intermediate states. Limited proteolysis reveals more resistance to cleavage compared to apoE3/E4. Taken together, the findings suggest that the CT domain modulates the lipid-binding ability of apoE and attenuates the overall dynamics of the protein, which bears direct relevance in regulation of lipoprotein metabolism with implications in amyloid-related neurodegeneration.

Genetic analysis of comorbidities between osteoarthritis, sarcopenia, and osteoporosis

BACKGROUND

Osteoarthritis (OA), sarcopenia (SCP), and osteoporosis (OP) pose a substantial global morbidity and mortality burden, and previous studies have observed potential associations among them. This study aims to comprehensively characterize the common genetic structure, biological basis, and underlying causal relationship among OA, SCP, and OP.

METHODS

We used pooled statistics from the largest European genome-wide association study to investigate the genetic overlap and underlying causal relationships among OA, SCP, and OP. LD Score Regression (LDSC) was first used for estimating global and local genetic associations, cross-trait meta-analysis was then conducted to identify shared loci, and mendelian randomization (MR) analysis was performed to test causal association.

RESULTS

In global and local genetic correlation analysis, we found strong positive correlations among OA, SCP, and OP. Cross-trait meta-analysis revealed 9 novel pleiotropic loci for HandOA_SCP trait-pairs, 1 for ThumbOA_SCP (females), and 6 for KneeOA_SCP (males)0.10 novel pleiotropic loci were also identified for HipOA_TBMD, while none for WLM_FinOP. Bidirectional MR analyses indicated significant causal associations between HandOA and SCP(Forward: OR: 1.41, 95 % CI: 1.25-1.60, p < 0.01,Reverse: OR: 1.77, 95 % CI: 1.34-2.35, p < 0.01). Reverse analyses suggested that ThumbOA.female (OR: 1.92, 95 % CI:1.18-3.13, p < 0.01) and KneeOA.male (OR: 1.58, 95 % CI: 1.13-2.12, p < 0.01) were positively correlated with SCP, while TBMD was positively correlated with HipOA (OR: 1.23, 95 % CI: 1.16-1.31, p < 0.01).

CONCLUSIONS

Our work demonstrates a shared genetic basis, pleiotropic loci, and putative causal relationships among OA, SCP, and OP, highlighting the intrinsic links behind these three complex skeletal diseases.

Insights into spinal muscular atrophy from molecular biomarkers

Spinal muscular atrophy is a devastating motor neuron disease characterized by severe cases of fatal muscle weakness. It is one of the most common genetic causes of mortality among infants aged less than 2 years. Biomarker research is currently receiving more attention, and new candidate biomarkers are constantly being discovered. This review initially discusses the evaluation methods commonly used in clinical practice while briefly outlining their respective pros and cons. We also describe recent advancements in research and the clinical significance of molecular biomarkers for spinal muscular atrophy, which are classified as either specific or non-specific biomarkers. This review provides new insights into the pathogenesis of spinal muscular atrophy, the mechanism of biomarkers in response to drug-modified therapies, the selection of biomarker candidates, and would promote the development of future research. Furthermore, the successful utilization of biomarkers may facilitate the implementation of gene-targeting treatments for patients with spinal muscular atrophy.

From genes to clinic: Genomic and cross-sectional cohort analysis of oxidative stressors and lipid metabolism in European ancestry

BACKGROUND

The link between oxidative stress and lipid metabolism is widely studied, but their causal relationship in the general population remains unclear.

METHODS

We utilized weighted regression and propensity score matching (PSM) models to investigate the relationship between endogenous oxidative stress markers (serum bilirubin and uric acid) and lipid metabolism in 11,087 participants of European ancestry from the National Health and Nutrition Examination Survey (NHANES) during the period from 2005 to 2018. Additionally, we performed a bidirectional two-sample Mendelian randomization (MR) analysis using Genome-Wide Association Study (GWAS) summary statistics from individuals of European ancestry (n = 997 to 575,531) to explore the genetic causal relationship between oxidative stress markers and lipid metabolism profiles (n = 20,430).

RESULTS

Weighted regression showed that serum uric acid significantly increased high cholesterol (OR = 1.11, 95 % CI = 1.06-1.15, P < 0.001) and high triglycerides (OR = 1.25, 95 % CI = 1.20-1.30, P < 0.001). PSM analysis confirmed that serum uric acid increased the incidence of high triglycerides (OR = 1.57, 95 % CI = 1.35-1.82, P < 0.001). Additionally, a strong bidirectional genetic relationship was found between oxidative stress markers and lipid metabolism. For example, serum uric acid increased serum triglycerides (β = 0.1904, Se = 0.05, P < 0.001) and decreased total cholesterol in very large HDL (β = -0.1298, Se = 0.039, P < 0.001). Conversely, total cholesterol reduced direct bilirubin levels (β = -0.1707, Se = 0.018, P < 0.001). No significant horizontal pleiotropy was detected by MR-Egger intercept.

CONCLUSION

Our findings demonstrate a robust genetic and population-based association between oxidative stress markers and lipid metabolism, suggesting potential therapeutic targets for lipid disorders based on endogenous oxidative stressors.

Diagnostic tools in respiratory medicine (Review)

Recent advancements in diagnostic technologies have significantly transformed the landscape of respiratory medicine, aiming for early detection, improved specificity and personalized therapeutic strategies. Innovations in imaging such as multi-slice computed tomography (CT) scanners, high-resolution CT and magnetic resonance imaging (MRI) have revolutionized our ability to visualize and assess the structural and functional aspects of the respiratory system. These techniques are complemented by breakthroughs in molecular biology that have identified specific biomarkers and genetic determinants of respiratory diseases, enabling targeted diagnostic approaches. Additionally, functional tests including spirometry and exercise testing continue to provide valuable insights into pulmonary function and capacity. The integration of artificial intelligence is poised to further refine these diagnostic tools, enhancing their accuracy and efficiency. The present narrative review explores these developments and their impact on the management and outcomes of respiratory conditions, underscoring the ongoing shift towards more precise and less invasive diagnostic modalities in respiratory medicine.

"We know what to do for you, but we can't do it:" How actionability is coordinated and contested in genomics research

Over the last few decades, an influential movement has emerged in genomics research advocating for the return of "actionable" findings to research participants. This movement argues that actionable findings constitute clinically significant information that can be used to inform preventive care, and that research projects may therefore have a responsibility to disclose such findings. Using a document analysis of institutional and expert guidance, this article traces how the notion of actionability became a predominant justification for the disclosure of research findings, and explores how this guidance has failed to account for local and structural coordination of actionability. The paper presents two case studies of US-based research projects, Geisinger Health System's MyCode Initiative and the National Institutes of Health's All of Us Research Program, to characterize how the disclosure of actionable findings has been implemented in research programs, and to reveal how a decontextualized approach to actionability threatens to undermine the promised clinical utility of genomic findings and exacerbate inequalities in healthcare access. As research projects increasingly adopt clinical actionability as a stand-in for clinical utility, exchanging evidence of improved health outcomes with opportunities for preventive interventions, coordination of the responsibilities and resources for realizing actionability is essential. This analysis indicates the possible consequences of contested actionability, and points to the need for further investigation of how actionable findings are implemented in practice.

Genetic insights into the role of mitochondria-related genes in mental disorders: An integrative multi-omics analysis

BACKGROUND

Mitochondrial dysfunction has been implicated in the development of mental disorders, yet the underlying mechanisms remain unclear. In this study, we employed summary-data-based Mendelian randomization (SMR) analysis to explore the associations between mitochondrial-related genes and seven common mental disorders across gene expression, DNA methylation, and protein levels.

METHOD

Summary statistics from genome-wide association studies were used for seven mental disorders, including attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder, anxiety, bipolar disorder, major depressive disorder, post-traumatic stress disorder, and schizophrenia (SCZ). Instrumental variables associated with 1136 mitochondria-related genes were derived from summary statistics for DNA methylation, gene expression, and protein quantitative trait loci. SMR analyses and colocalization analyses were then conducted across these three biological levels to explore the associations with each of the seven mental disorders.

RESULTS

We identified mitochondria-related genes associated with mental disorders with multi-omics evidence: RMDN1 for ADHD, and ACADVL, ETFA, MMAB, and PPA2 for SCZ. Specifically, an increase of one standard deviation in the level of RMDN1 was linked to a 12 % decrease in the risk of developing ADHD (OR = 0.88, 95 % CI: 0.83-0.94). Increased levels of ETFA (OR = 1.79, 95 % CI: 1.24-2.60) and MMAB (OR = 1.10, 95 % CI: 1.05-1.16) were significantly associated with increased risk of SCZ. Conversely, high levels of ACADVL (OR = 0.50, 95 % CI: 0.33-0.77) and PPA2 (OR = 0.68, 95 % CI: 0.55-0.85) were associated with a reduced risk of SCZ.

CONCLUSIONS

These findings suggested that dysfunction in mitochondria-related genes may underlie the molecular mechanisms of ADHD and SCZ, providing novel biomarkers for diagnosis and therapeutic interventions.

Clonal hematopoiesis of indeterminate potential: recent developments and perspectives

PURPOSE OF REVIEW

This review encompasses the recently published information on clonal hematopoiesis of indeterminate potential (CHIP) and discusses its future prospects. By announcing advances in the research of CHIP risk factors and related diseases, with the purpose of offering new insights to treat both hematologic and nonhematologic disorders.

RECENT FINDINGS

The majority of studies have shown that CHIP is a common biological condition associated with aging and the incidence of clonal hematopoiesis increases with age. The pathophysiology of blood diseases is projected to be significantly influenced by CHIP. Nevertheless, increasing studies have expanded the application of CHIP to cover nonhematologic diseases such as cardiovascular, renal, liver, and pulmonary diseases. Furthermore, with the fast advancement of genetic testing technology and preventive medicine, the involvement of CHIP in a variety of disorders shows promise as an essential target for preventing disease onset and progression.

SUMMARY

CHIP is linked to a variety of illnesses and has a significant influence on an individual's health outlook. Thus, identifying and managing CHIP is critical for improving the clinical results of the individuals concerned.

Molecular and functional characterization of peptidoglycan recognition protein-L2 from Hexagrammos otakii (Ho-PGRP-L2) involved in innate immune response

Peptidoglycan recognition proteins (PGRPs), a family of pattern recognition receptors, play diverse roles in antimicrobial defense. This study investigated the role of a long-type peptidoglycan recognition protein designated as Ho-PGRP-L2 in the antibacterial immune response of the economically important fish species Hexagrammos otakii. Ho-PGRP-L2 was successfully cloned and characterized, which possesses a signal peptide, a typical PGRP domain, and a Zn2+ binding domain including four specific amino acid residues which were required for amidase activity. The qRT-PCR analysis revealed that Ho-PGRP-L2 was predominantly expressed in the liver, with very low levels in the other tissues. The recombinant Ho-PGRP-L2 protein (rHo-PGRP-L2) exhibited polysaccharide-binding, bacteria-binding, bacteria agglutinating, amidase, and antibacterial activities, indicating its function as a recognizer and effector within the antibacterial immune response. Additionally, rHo-PGRP-L2 enhanced phagocyte chemotaxis, indicating its role as an 'immune activator'. These findings indicated that Ho-PGRP-L2 of H. otakii was involved in host defense against bacterial infections, laying a foundation for developments in H. otakii aquaculture disease management.

Investigating the binding products between human apolipoproteins and oxidized 1-palmitoyl-2-arachidonyl-sn-glycerol-3-phosphocholine by micellar electrokinetic chromatography

A micellar electrokinetic chromatography (MEKC) method has been developed to investigate the binding products between human apolipoproteins (Apos) and oxidized 1-palmitoyl-2-arachidonoyl-sn‑glycero-3-phosphocholine (ox-PAPC) products. The optimal MEKC separation buffer was composed of a solution mixture of 10 mM sodium phosphate, 50 mM bile salts (50 % sodium cholate and 50 % sodium deoxycholate), 30 % (v/v)1-propanol and 70 % (v/v) water, pH 7.4. The optimal MEKC sample buffer was composed of 70 % (v/v) PBS buffer and 30 % (v/v) MeOH. The selected separation voltage was 20 kV, and the capillary temperature was 25℃. The MEKC profiles of ox-PAPC products showed good separations and repeatability. The MEKC profiles of apos and their binding products also showed good repeatability. For the analysis of native PAPC (n-PAPC), the method is linear in the range of 0.00-6.00 mg/mL with a correlation coefficient 0.9984. The concentration limit of detection (LOD) is 0.29 mg/mL. The concentration limit of quantitation (LOQ) is 0.98 mg/mL. The binding reactions between several important human apolipoproteins (Apos A-I, A-II, C-I, C-II, C-III and E) and native PAPC, ox-PAPC products have been investigated. The concentrations of Apos and ox-PAPC products for binding reactions have been examined. The optimal binding buffer selected was 70 % (v/v) PBS buffer and 30 % (v/v) MeOH. The binding reaction was performed at 37 ℃ for 3 hr. The results indicated that ox-PAPC products bound to Apos A-I, A-II, C-I, and E more strongly than n-PAPC. However, both ox-PAPC products and n-PAPC did not bind to Apos C-II and C-III strongly. The results suggested pro-inflammatory properties of Apos A-I, A-II, C-I, and E, and implied one of the molecular mechanisms resulting in dysfunctional HDL particles. This study also demonstrated the feasibility of investigating the binding reactions between human apolipoproteins and ox-PAPC products by MEKC.

Physiological implications of the Slack channel in the central and peripheral nervous systems

The Slack channels, encoded by KCNT1, are found in neurons across the central nervous system (CNS) and peripheral nervous system (PNS), generating a delayed outward current known as sodium-activated potassium current (IKNa). IKNa plays a crucial role in shaping neuronal excitability and facilitating adaptation in response to sustained stimulation. Slack channels are crucial for neural plasticity and cognitive function; however, mutations in these channels cause profound learning and developmental abnormalities in humans. The physiological significance of Slack conductance in both systems is still unclear. This review provides a comprehensive overview of the role of Slack channels in both CNS and PNS, along with their associated modulators. It offers a summary of diseases that can result from abnormal expression of the Slack channel in both systems. Furthermore, identifying potent blockers and activators of Slack channels could greatly improve our understanding of Slack functions.

Integrating explainable machine learning and transcriptomics data reveals cell-type specific immune signatures underlying macular degeneration

Genome-wide association studies (GWAS) have established key role of immune dysfunction in Age-related Macular Degeneration (AMD), though the precise role of immune cells remains unclear. Here, we develop an explainable machine-learning pipeline (ML) using transcriptome data of 453 donor retinas, identifying 81 genes distinguishing AMD from controls (AUC-ROC of 0.80, CI 0.70-0.92). Most of these genes were enriched in their expression within retinal glial cells, particularly microglia and astrocytes. Their role in AMD was further strengthened by cellular deconvolution, which identified distinct differences in microglia and astrocytes between normal and AMD. We corroborated these findings using independent single-cell data, where several ML genes exhibited differential expression. Finally, the integration of AMD-GWAS data identified a regulatory variant, rs4133124 at PLCG2, as a novel AMD association. Collectively, our study provides molecular insights into the recurring theme of immune dysfunction in AMD and highlights the significance of glial cell differences in AMD progression.

Eosinophilic gastroenteritis in a 14-year-old patient with Noonan syndrome with a PTPN11 variation: a case report

BACKGROUND

Noonan syndrome has a wide range of symptoms due to dysregulation of the RAS/MAPK pathway with several gene variations, including the PTPN11 gene. There are currently no case reports of Noonan syndrome with eosinophilic gastroenteritis.

CASE

A 14-year-old Japanese girl was clinically diagnosed with Noonan syndrome. She had intermittent abdominal pain and vomiting from 10 years old. The patient was diagnosed with eosinophilic gastroenteritis on the basis of the pathological finding of multiple foci with > 20 eosinophils/high power field in the mucosal lamina propria of the colon by endoscopy at 12 years old. Vomiting and abdominal pain are currently being controlled by antihistamines and leukotriene antagonist therapy. Genetic testing showed the missense variation p.Ala72Gly in the PTPN11 gene.

DISCUSSION

The pathogenesis of eosinophilic gastroenteritis is similar to that of other allergic inflammatory diseases, such as bronchial asthma. The cause of eosinophilic gastroenteritis is multifactorial, including genetic and environmental factors. The PTPN11 gene variations are suggested to promote eosinophilic disorders by leading to the activation of the RAS/MAPK pathway. This activation subsequently results in the production of interleukin-5, which plays a crucial role in the pathogenesis of eosinophilic gastroenteritis. The relationship between eosinophilic gastroenteritis and the PTPN11 gene has not yet been reported.

CONCLUSION

We herein present the first known case of eosinophilic gastroenteritis in Noonan syndrome with a variation in the PTPN11 gene. The relationship between Noonan syndrome and eosinophilic gastroenteritis remains unknown; therefore, additional case reports of Noonan syndrome with eosinophilic gastroenteritis are required to elucidate this potential relationship.

EZH2 inhibition and 5-azacytidine enhance antitumor immunity in PTEN-deficient glioblastoma by activation viral mimicry response

BACKGROUND

PTEN-deficient glioblastoma (GBM) is characterized by an immunosuppressive tumor microenvironment (TME), therapeutic resistance, and poor prognosis. Emerging evidence suggests that dysregulation of the endogenous retrovirus (ERV)-MAVS-IFN pathway may contribute to immune evasion in cancer, but its role in PTEN-deficient GBM remains unclear.

METHODS

Using flow cytometry and single-cell RNA sequencing, we analyzed the immune landscape of PTEN-deficient GBM. We evaluated the effects of 5-azacytidine (5-AZA) monotherapy and its combination with EZH2 inhibition (EZH2i) on ERV reactivation, type I interferon (IFN) responses, and TME remodeling. Mechanistic studies focused on H3K27me3-mediated epigenetic regulation of ERV expression.

RESULTS

We found that PTEN deficiency suppresses type I IFN responses by impairing viral mimicry through dysregulation of the ERV-MAVS-IFN pathway, thereby sustaining an immunosuppressive TME. While 5-AZA alone failed to reactivate ERVs or overcome therapeutic resistance, combining it with EZH2i synergistically restored robust type I IFN signaling. This combination therapy reduced H3K27me3 levels, promoting ERV transcriptional activation and enhancing 5-AZA-induced viral mimicry. Consequently, the dual treatment reprogrammed the TME to boost antitumor immunity and suppress tumor progression.

CONCLUSIONS

Our study demonstrates that PTEN-deficient GBM evades immune surveillance by suppressing the ERV-MAVS-IFN axis. The combination of EZH2i and 5-AZA overcomes this resistance by epigenetically reactivating viral mimicry, offering a promising therapeutic strategy to enhance antitumor immunity and improve outcomes in patients with PTEN-deficient GBM.

MPSE identifies newborns for whole genome sequencing within 48 h of NICU admission

Identifying critically ill newborns who will benefit from whole genome sequencing (WGS) is difficult and time-consuming due to complex eligibility criteria and evolving clinical features. The Mendelian Phenotype Search Engine (MPSE) automates the prioritization of neonatal intensive care unit (NICU) patients for WGS. Using clinical data from 2885 NICU patients, we evaluated the utility of different machine learning (ML) classifiers, clinical natural language processing (CNLP) tools, and types of Electronic Health Record (EHR) data to identify sick newborns with genetic diseases. Our results show that MPSE can identify children most likely to benefit from WGS within the first 48 h after NICU admission, a critical window for maximally impactful care. Moreover, MPSE provided stable, robust means to identify these children using many combinations of classifiers, CNLP tools, and input data types-meaning MPSE can be used by diverse health systems despite differences in EHR contents and IT support.

Navigating the Paradox of Senescence and Chemoresistance in Pancreatic Cancer

Cellular senescence, described as a mechanism of irreversible cell cycle arrest, has emerged as a complex and multifaceted process with significant implications in cancer biology, particularly in pancreatic ductal adenocarcinoma (PDAC). This literature review aims to explore the intricate role of senescence in PDAC, focusing on its dual nature during tumorigenesis, in addition to therapy resistance, and its potential as a therapeutic target. Senescence escape was found to play a crucial role in PDAC progression, prompting the development of various pro-senescence therapies. However, recent studies have revealed a paradoxical aspect of the senescence-associated secretory phenotype, revealing its pro-tumorigenic effects and contribution to immune evasion in PDAC. By integrating insights from recent molecular studies, this review synthesizes current knowledge on the role of senescence in PDAC tumorigenesis and chemoresistance, with an emphasis on the emerging role of the tumor microenvironment and explores current and promising avenues for future research and potential therapeutic interventions.

Methods in quantitative biology-from analysis of single-cell microscopy images to inference of predictive models for stochastic gene expression

The field of quantitative biology (q-bio) seeks to provide precise and testable explanations for observed biological phenomena by applying mathematical and computational methods. The central goals of q-bio are to (1) systematically propose quantitative hypotheses in the form of mathematical models, (2) demonstrate that these models faithfully capture a specific essence of a biological process, and (3) correctly forecast the dynamics of the process in new, and previously untested circumstances. Achieving these goals depends on accurate analysis and incorporating informative experimental data to constrain the set of potential mathematical representations. In this introductory tutorial, we provide an overview of the state of the field and introduce some of the computational methods most commonly used in q-bio. In particular, we examine experimental techniques in single-cell imaging, computational tools to process images and extract quantitative data, various mechanistic modeling approaches used to reproduce these quantitative data, and techniques for data-driven model inference and model-driven experiment design. All topics are presented in the context of additional online resources, including open-source Python notebooks and open-ended practice problems that comprise the technical content of the annual Undergraduate Quantitative Biology Summer School (UQ-Bio).

Advances in CRISPR-Cas9 in lineage tracing of model animals

Cell lineage tracing is a key technology for describing the developmental history of individual progenitor cells and assembling them to form a lineage development tree. However, traditional methods have limitations of poor stability and insufficient resolution. As an efficient and flexible gene editing tool, CRISPR-Cas9 system has been widely used in biological research. Furthermore, CRISPR-Cas9 gene editing-based tracing methods can introduce fluorescent proteins, reporter genes, or DNA barcodes for high-throughput sequencing, enabling precise lineage analysis, significantly improving precision and resolution, and expanding its application range. In this review, we summarize applications of CRISPR-Cas9 system in cell lineage tracing, with special emphasis on its successful applications in traditional model animals (e.g., zebrafish and mice), large animal models (pigs), and human cells or organoids. We also discussed its potential prospects and challenges in xenotransplantation and regenerative medicine.

Vision & the Ageing Surgeon: A Review

Populations in the developed world are ageing and their surgeons are no exception. Accurate vision is essential for the surgeon to operate effectively, yet optimal vision has an expiry date in advancing age. This review examines the effects of ageing on the eye with particular focus on the visual changes of significance to senior surgeons who currently account for 20%-25% of the surgeon workforce. The major age-related diseases of the eye, which include cataracts, glaucoma, age-related macular degeneration and diabetic retinopathy, are surmised; together with physiologic ocular changes that accompany normal ageing, including loss of accommodation (presbyopia), reduced pupil size (senile miosis), reduced contrast sensitivity, and impaired binocular vision, amongst others. The aforementioned conditions may impair operative visualisation in the elderly surgeon and potentially impact surgical performance. Strategies and available technologies that support operative visualisation-particularly magnification aids, illumination systems and fluorescent dyes in surgery-are appraised with consideration to the senior surgeon who may be affected by the aforementioned visual changes associated with ageing. To inform minimum standards of visual function for safe surgical practice, future prospective studies are needed which report on individual surgeon-related measures of visual function together with postoperative outcomes. This vein of future research will allow for an evidence-based evaluation of proposed safety measures for which the data are currently lacking, thereby providing clarity regarding whether requisite age-based visual assessments improve surgical outcomes, and if so, at what age and frequency should such evaluations take place.

cGAS-STING are responsible for premature aging of telomerase-deficient zebrafish

Telomere shortening occurs in multiple tissues throughout aging. When telomeres become critically short, they trigger DNA-damage responses and p53 stabilization, leading to apoptosis or replicative senescence. In vitro, cells with short telomeres activate the cGAS-STING innate immune pathway resulting in type-I interferon-based inflammation and senescence. However, the consequences of these events for the organism are not yet understood. Here, we show that sting is responsible for premature aging of telomerase-deficient zebrafish. We generated sting-/- tert-/- double-mutant animals and observed a thorough rescue of tert-/- phenotypes. At the cellular level, lack of cGAS-STING in tert mutants resulted in reduced senescence, increased cell proliferation, and decreased inflammation despite similarly short telomeres. Critically, absence of sting function resulted in dampening of the DNA damage response and reduced p53 levels. At the organism level, sting-/- tert-/- zebrafish regained fertility, showed delayed cachexia, and decreased cancer incidence, resulting in increased healthspan and lifespan of telomerase mutant animals.

SEQSIM: A novel bioinformatics tool for comparisons of promoter regions-a case study of calcium binding protein spermatid associated 1 (CABS1)

BACKGROUND

Understanding transcriptional regulation requires an in-depth analysis of promoter regions, which house vital cis-regulatory elements such as core promoters, enhancers, and silencers. Despite the significance of these regions, genome-wide characterization remains a challenge due to data complexity and computational constraints. Traditional bioinformatics tools like Clustal Omega face limitations in handling extensive datasets, impeding comprehensive analysis. To bridge this gap, we developed SEQSIM, a sequence comparison tool leveraging an optimized Needleman-Wunsch algorithm for high-speed comparisons. SEQSIM can analyze complete human promoter datasets in under an hour, overcoming prior computational barriers.

RESULTS

Applying SEQSIM, we conducted a case study on CABS1, a gene associated with spermatogenesis and stress response but lacking well-defined functions. Our genome-wide promoter analysis revealed 41 distinct homology clusters, with CABS1 residing within a cluster that includes promoters of genes such as VWCE, SPOCK1, and TMX2. These associations suggest potential co-regulatory networks. Additionally, our findings unveiled conserved promoter motifs and long-range regulatory sequences, including LINE-1 transposable element fragments shared by CABS1 and nearby genes, implying evolutionary conservation and regulatory significance.

CONCLUSIONS

These results provide insight into potential gene regulation mechanisms, enhancing our understanding of transcriptional control and suggesting new pathways for functional exploration. Future studies incorporating SEQSIM could elucidate co-regulatory networks and chromatin interactions that impact gene expression.

Causal mediation of plasma metabolomics in pancreatitis: A Mendelian randomization study

Pancreatitis frequently leads to hospital stay for digestive system disorders and is in high demand for treatment. To identify possible treatment targets, we utilized Mendelian randomization (MR) to investigate the potential causal effects of metabolites on the outcomes of pancreatitis and examined the intermediary roles of risk factors associated with pancreatitis. We gathered GWAS data on 1091 plasma metabolites and 319 metabolite ratios, along with risk factors and phenotypes associated with pancreatitis and its subtypes. Risk factors included H, T2DM, body mass index (BMI), HLP, cholelithiasis, and Inflammatory bowel disease (IBD). Phenotypic outcomes encompassed acute pancreatitis (AP), chronic pancreatitis, alcohol-induced acute pancreatitis, and alcohol-induced chronic pancreatitis. To test the robustness of the findings, we estimated causality using inverse-variance-weighted MR complemented by sensitivity analyses. Additionally, we performed reverse MR analysis to explore potential reverse causality. This study identified 53 plasma metabolites and 22 metabolite ratios predicted by genetics that were significantly associated with pancreatitis (P < .05). Additionally, 54 metabolite ratios and 193 metabolites were associated with pancreatitis risk factors, with 86 and 27 metabolites, respectively, showing significant associations. The MR analysis confirmed that BMI, IBD, and HLP as pancreatitis risk factors (P < .05). It was also revealed that BMI and IBD mediate the relationship between certain metabolite levels and pancreatitis. The identified metabolites and their ratios have the potential to serve as circulating biomarkers with promising applications in CP screening and prevention strategies.

A versatile CRISPR/Cas9 system off-target prediction tool using language model

Genome editing with the CRISPR/Cas9 system has revolutionized life and medical sciences, particularly in treating monogenic genetic diseases by enabling long-term therapeutic effects from a single intervention. However, the CRISPR/Cas9 system can tolerate mismatches and DNA/RNA bulges at target sites, leading to unintended off-target effects that pose challenges for gene-editing therapy development. Existing high-throughput detection and in silico prediction methods are often limited to specifically designed single guide RNAs (sgRNAs) and perform poorly on unseen sequences. To address these limitations, we introduce CCLMoff, a deep learning framework for off-target prediction that incorporates a pretrained RNA language model from RNAcentral. CCLMoff captures mutual sequence information between sgRNAs and target sites and is trained on a comprehensive, updated dataset. This approach enables accurate off-target identification and strong generalization across diverse NGS-based detection datasets. Model interpretation reveals the biological importance of the seed region, underscoring CCLMoff's analytical capabilities. The development of CCLMoff lays the foundation for a comprehensive, end-to-end sgRNA design platform, enhancing both the precision and efficiency of CRISPR/Cas9-based therapeutics. CCLMoff is a versatile tool and is publicly available at github.com/duwa2/CCLMoff .

Parents' perspectives on expanded newborn genomic screening in Abu Dhabi, United Arab Emirates

BACKGROUND

Newborn genomic screening offers the potential for early detection and management of genetic disorders. Understanding parental perspectives is essential before integrating genomic testing into standard newborn screening.

METHODS

This was a descriptive cross-sectional study surveyed 568 parents in Abu Dhabi, United Arab Emirates (UAE). An online self-administered validated and piloted questionnaire was used to gather information on demographic characteristic and perspectives regarding newborn genomic screening. Data were analysed using R version 4.4.3.

RESULTS

Most parents (78.2%) supported integrating genomics into newborn screening programs, with 63.5% stating it requires distinct management from standard screening. Females preferred geneticists (38.2% vs. 32.5%, p < 0.001) and hospitals (45.1% vs. 39.2%, p < 0.001) for discussions, with 74.2% emphasizing explicit consent compared to 68.5% of males (p < 0.002). Treatability (82.7%), age of symptom onset (74.1%), and severity (72.2%) were key decision-making factors. Additionally, 66.7% preferred genomic testing to be covered by insurance, and 82.2% supported storing genomic data for future use.

CONCLUSION

Parents participated in the study strongly support genomic newborn screening. Gender-based differences emphasize the need for tailored communication and culturally sensitive strategies to inform policy development and implementation of newborn genomic screening program in the UAE and similar contexts.

Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays

We describe a DNA-array-based method to infer intramolecular connections in a population of RNA molecules in vitro. First we add DNA oligonucleotide "patches" that perturb the RNA connections, and then we use a microarray containing a complete set of DNA oligonucleotide "probes" to record where perturbations occur. The pattern of perturbations reveals couplings between regions of the RNA sequence, from which we infer connections as well as their prevalences in the population, without reference to folding models. We validate this patch-probe method using the 1058-nucleotide RNA genome of satellite tobacco mosaic virus (STMV), which has been shown to have multiple long-range connections. Our results not only indicate long-range connections that agree with previous structures but also reveal the prevalence of competing connections. Together, these results suggest that multiple structures with different connectivity coexist in solution. Furthermore, we show that the prevalence of certain connections changes when pseudouridine, an important component of natural and synthetic RNAs, is substituted for uridine in STMV RNA, and that the connectivity of STMV minus strands is qualitatively distinct from that of plus strands. Finally, we use a simplified version of the method to validate a predicted 317-nucleotide connection within the 3569-nucleotide RNA genome of bacteriophage MS2.

Decoding tissue complexity: multiscale mapping of chemistry-structure-function relationships through advanced visualization technologies

Comprehensively acquiring biological tissue information is pivotal for advancing our understanding of biological systems, elucidating disease mechanisms, and developing innovative clinical strategies. Biological tissues, as nature's archetypal biomaterials, exhibit multiscale structural and functional complexity that provides critical principles for synthetic biomaterials. Tissues/organs integrate molecular, biomechanical, and hierarchical architectural features across scales, offering a blueprint for engineering functional materials capable of mimicking or interfacing with living systems. Biological visualization technologies have emerged as indispensable tools for decoding tissue complexity, leveraging their unique technical advantages and multidimensional analytical capabilities to bridge the gap between macroscopic observations and molecular insights. The integration of cutting-edge technologies such as artificial intelligence (AI), augmented reality, and deep learning is revolutionizing the field and enabling real-time, high-resolution, and predictive analyses that transcend the limitations of traditional imaging modalities. This review systematically explores the principles, applications, and limitations of state-of-the-art biological visualization technologies, with a particular emphasis on the transformative advancements in AI-driven image analysis, multidimensional imaging and reconstruction, and multimodal data integration. By analyzing these technological trends, we envision a future where biological visualization evolves towards greater intelligence, multidimensionality, and multiscale precision, offering unprecedented theoretical and methodological support for deciphering tissue complexity and further advancing biomaterials development. These advancements promise to accelerate breakthroughs in precision medicine, tissue engineering, and therapeutic development, ultimately reshaping the landscape of biomedical research and clinical practice.

The Role of the AGPAT2 Gene in Adipose Tissue Biology and Congenital Generalized Lipodystrophy Pathophysiology

1-Acylglycerol-3-phosphate O-acyltransferase (1-AGPAT) is an enzyme family composed of 11 isoforms. Notably, 1-AGPAT 2, the most studied isoform since its discovery, is a critical enzyme in the triglyceride synthesis pathway, converting lysophosphatidic acid to phosphatidic acid. In addition, AGPAT2 gene expression is shown to be essential for adipocyte development and maturation. Defects in AGPAT2 are responsible for significant pathophysiological alterations related to adipose tissue (AT). Pathogenic variants in this gene are the molecular etiology of Congenital Generalized Lipodystrophy type 1 (CGL1), in which fatty tissue is absent from birth. Metabolically, these individuals have several metabolic complications, including hypoleptinemia, hypoadiponectinemia, hyperglycemia, and hypertriglyceridemia. Furthermore, numerous AGPAT2 pathogenic variants that enormously affect the amino acid sequence, the tertiary structure of 1-AGPAT 2, and their transmembrane and functional domains were found in CGL1 patients. However, studies investigating the genotype-phenotype relationship in this disease are scarce. Here, we used bioinformatics tools to verify the effect of the main pathogenic variants reported in the AGPAT2 gene: c.366-588del, c.589-2A>G, c.646A>T, c.570C>A, c.369-372delGCTC, c.202C>T, c.514G>A, and c.144C>A in the 1-AGPAT 2 membrane topology. We also correlated the phenotype of CGL1 subjects harboring these variants to understand the genotype-phenotype relationship. We provided an integrative view of clinical, genetic, and metabolic features from CGL1 individuals, helping to understand the role of 1-AGPAT 2 in the pathogenesis of this rare disease. Data reviewed here highlight the importance of new molecular studies to improve our knowledge concerning clinical and genetic heterogeneity in CGL1.

Enhancing Biosecurity in Mollusc Aquaculture: A Review of Current Isothermal Nucleic Acid Detection Methods

The growing human population has increased the need for food beyond what terrestrial sources can provide. This boosts aquaculture demand for molluscs, fish, and crustaceans. Molluscs are popular for their nutritional benefits, making them a profitable industry. Despite a 3% annual growth in mollusc populations, recent high mortality rates and population losses due to poor feeding practices and water pollution have made them more disease-prone. Limited treatment options exist for mollusc diseases in aquaculture systems. Hence, developing rapid, sensitive, and cost-effective diagnostic tools for field use is essential to identify and prevent infections promptly. Recently developed isothermal nucleic acid amplification technologies, like loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), offer rapid results within an hour. This review examines these isothermal diagnostic techniques for mollusc pathogens and their potential for field application.

A common computational and neural anomaly across mouse models of autism

Computational psychiatry studies suggest that individuals with autism spectrum disorder (ASD) inflexibly update their expectations. Here we leveraged high-yield rodent psychophysics, extensive behavioral modeling and brain-wide single-cell extracellular recordings to assess whether mice with different genetic perturbations associated with ASD show this same computational anomaly, and if so, what neurophysiological features are shared across genotypes. Mice harboring mutations in Fmr1, Cntnap2 or Shank3B show a blunted update of priors during decision-making. Compared with mice that flexibly updated their priors, inflexible updating of priors was associated with a shift in the weighting of prior encoding from sensory to frontal cortices. Furthermore, frontal areas in mouse models of ASD showed more units encoding deviations from the animals' long-run prior, and sensory responses did not differentiate between expected and unexpected observations. These findings suggest that distinct genetic instantiations of ASD may yield common neurophysiological and behavioral phenotypes.

Current gaps in knowledge and future research directions for Aboriginal and Torres Strait Islander children with cancer

Paediatric cancer is the leading cause of disease-related death in Australian children. Limited research focuses on cancer in Aboriginal and Torres Strait Islander children. Although there appears to be a lower incidence of cancer overall in Aboriginal and Torres Strait Islander children compared with non-Indigenous children, a high proportion of Aboriginal and Torres Strait Islander children are diagnosed with acute myeloid leukaemia. Five-year overall survival is lower for many cancer types in Aboriginal and Torres Strait Islander children. There is a need for Indigenous-specific research focused on molecular and genetic profiles, pharmacogenomics and survivorship, both within Australia and globally. Future research in this space should be co-designed and led by Aboriginal and Torres Strait Islander communities; alongside clinicians, researchers and services to ensure that the priorities of Aboriginal and Torres Strait Islander people are met.

Ocular Characteristics and Genotype-Oriented Disease Spectrum of Alström Syndrome in Taiwan

Purpose

This study aimed to describe the ophthalmological features of Alström syndrome, a rare syndromic ciliopathy, and to delineate the genotype-associated disease spectrum.

Methods

Eight Taiwanese patients were recruited for this study. Pathogenic variants were identified using next-generation sequencing, and medical records were reviewed for systemic involvement. Best-corrected visual acuity, cycloplegic refraction, blue light fundus autofluorescence imaging, International Society for Clinical Electrophysiology of Vision-standard full-field flash electroretinography, optical coherence tomography, and visual field testing were obtained and studied retrospectively.

Results

Common ocular manifestations included hyperopia, nystagmus, photophobia, and visual impairment. Most patients also exhibited obesity, sensorineural hearing loss, and developmental delays. Phenotype variability was observed in age of onset (0-8 years), severity of visual impairment, and extent of extraocular involvement. Electroretinography results reflected varying degrees of retinal degeneration. We identified c.11110_11128del as a genotype frequently occurring in Asian populations that demonstrated a more severe phenotype within our cohort. In addition, we discovered three novel variants, including a LINE-1 insertion in exon 8 (c.3565insL1), c.6166_6167insAT, and 8077del.

Conclusions

Alström syndrome may manifest with early-onset ocular and syndromic features, or demonstrate a later onset with limited extraocular involvement. This is the first report of a LINE-1 insertion in ALMS1, with affected patients exhibiting comparatively mild phenotypes.

Translational Relevance

Combined ophthalmological and extraocular phenotypes combined may aid in diagnosing this rare disease and differentiating it from other possible causes.

A National Study Among Diverse US Populations of Exposure to Prescription Medications with Evidence-Based Pharmacogenomic Information

Tailoring pharmacogenomic (PGx) implementation to diverse populations is vital to promoting health equity. We assessed prescriptions for medications with potentially actionable PGx information to identify patient characteristics associated with differential PGx medication exposure. We analyzed the nationally-representative MEPS dataset of adults who reported receiving prescriptions between 2014 and 2021. PGx medications include those the FDA and CPIC designate as having drug-gene associations supported by scientific evidence. With the primary outcome being PGx prescriptions, we performed Poisson regression adjusted for all other relevant covariates. In our final population (N = 119,722, 72% White/20% Black/4% Asian/8% Hispanic), 61% were prescribed a PGx medication, 56% were female, and 97% held health insurance coverage. Adults with private health insurance (65%) or public Medicaid/Medicare coverage (32%) were more likely to have PGx prescriptions than the uninsured (3%). Individuals with cardiovascular conditions [adjusted IRR (aIRR) = 1.45, 95% CI 1.41, 1.48], high cholesterol [aIRR = 1.37, 95% CI 1.35, 1.40], high blood pressure [aIRR = 1.14, 95% CI 1.12, 1.16], and cancer [aIRR = 1.02, 95% CI 1.00, 1.04] were more likely to receive PGx prescriptions. Self-reported Blacks were less likely than Whites to receive PGx medications [aIRR = 0.92, 95% CI 0.90, 0.94], and among those with health conditions, the likelihood of PGx medication exposure for underrepresented groups (Blacks, Hispanics, and Asians) was lower than for Whites. Our study using a comprehensive list of PGx medications in a nationally representative dataset indicates that certain populations are differentially exposed to genomically informed medications. This may suggest that if implementing a pharmacogenomics program based on reactive testing initiated by a prescription, a small underrepresentation of the Black population could be expected because of an underlying prescription disparity. Secondly, if implementing a pharmacogenomics program based on targeted preemptive testing, using clinical indication/comorbidity may be a reasonable way to enrich the population for prescriptions that would benefit from genotype tailoring.

Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins

This work presents a comprehensive investigation of sequence variations at human 5' splice sites (5'ss), exploring their impact on 5'ss strength and predicted splicing regulatory protein (SRP) binding. Leveraging 44 high-quality genomes, with fully haplotyped assemblies, we were able to fully assess homozygous and heterozygous sequence variations around and within 5'ss. Variations showed differing tolerance levels in protein-coding and non-coding transcripts. Around half of 5'ss variations did not alter 5'ss strength (measured by the HBond score, that estimates binding of the 11 nucleotides at the free U1 spliceosomal RNA 5' end). Heterozygous variations resulted in stronger 5'ss strength reductions and less compensatory effects of multiple sequence variations at the same 5'ss, compared to homozygous variations. Additionally, we observed a slight balance between changes in 5'ss strength and predicted SRP binding. Strong 5'ss (HBond score >18.8) showed strength variations in both directions, as theoretically expected for random distributions, whereas weaker 5'ss consistently showed lower strength reductions than expected or achievable. Variations at 5'ss of essential genes were less frequent than in other genes and showed a higher amount of variations that did not alter 5'ss strength. Acceptable changes in predicted SRP binding sites were highly dependent on their respective 5'ss strength.

Berberine promotes apoptosis and inhibits the migration of oral squamous carcinoma cells through inhibition of the RAGE/PI3K/AKT/mTOR pathway

Given the high recurrence rate, elevated risk of metastasis, and drug resistance associated with oral squamous cell carcinoma (OSCC), the development of low - toxicity and highly efficient therapeutic agents has emerged as a top research priority. In this study, we conducted an in-depth investigation into the efficacy and underlying mechanism of berberine (BBR), a compound renowned for its broad anticancer activity, in the context of OSCC. Using network pharmacology, we identified 91 potential targets of BBR in OSCC, with SRC, PIK3CA, and CDC42 ranking among the top. KEGG pathway analysis indicated that the cross-targets were predominantly concentrated in signaling pathways such as PI3K/AKT, AGE-RAGE, and Ras. Molecular docking assays demonstrated that the binding energies between BBR and the core targets were all below -5 kcal/mol, signifying favorable binding interactions. Bioinformatics studies unveiled that SRC, PIK3CA, and CDC42 were highly expressed in OSCC patients and correlated with a poorer prognosis. In vitro, experiments further substantiated that BBR impeded the proliferation and migration of OSCC cells and reduced the intracellular expression levels of RAGE, p-PI3K, p-AKT, and p-mTOR proteins. Our results suggest that BBR effectively facilitates apoptosis and curbs the proliferation and migration of OSCC, potentially by suppressing the RAGE/PI3K/AKT/mTOR pathway. In summary, these findings underscore the potential of BBR as a single agent capable of exerting multi-target and multi-pathway synergistic effects on cancer cells.