Single-cell Transcriptome-wide Mendelian Randomization and Colocalization Converge on Astrocytic TRIM66 as a Candidate Driver and Potential Therapeutic Target for Trigeminal Neuralgia.
Aug 2026· Current Medicinal Chemistry· Vol 33· 0 citations
Medicine
TL;DR
Astrocyte-specific regulation of TRIM66 may contribute to TN pathogenesis through neuroinflammatory pathways, offering a cell-type-resolved mechanistic perspective that complements existing models of TN biology.
Abstract
Background
Trigeminal Neuralgia (TN) is a disabling facial pain disorder with suboptimal pharmacological and surgical options. We hypothesized that genetic regulation of gene expression in specific brain cell types contributes to TN susceptibility and could nominate tractable therapeutic targets.
Methods
Single-cell cis-eQTLs from 183 neuropathology-free donors were used to instrument cell-type-specific expression. Variants surpassing genome-wide significance (P < 5×10-8) were LD-pruned (1000 Genomes Phase 3 European; r2 < 0.001; 10-Mb window) and harmonized; instruments with F < 10 were excluded. The final set comprised 1,746 Single Nucleotide Polymorphisms (SNPs) mapping to 1,745 eGenes. Two-Sample Mendelian Randomization (TwoSampleMR, R) tested eight brain cell types against TN risk in FinnGen (Release 12; 2,226 cases; 435,371 controls). Wald ratios were used for single-SNP instruments and inverse-variance weighting for multiple instruments. False Discovery Rate (FDR) control was applied within cell type. Colocalization (coloc, R) assessed shared causal variants.
Results
After pruning, 1,745 eGenes were analyzed across eight cell types. A single signal met within multiple-testing control: higher astrocytic Tripartite motif-containing 66 (TRIM66) expression associated with increased TN risk (Wald ratio; β = 0.3038, standard error (SE) = 0.0884, P = 5.87×10-4; odds ratio (OR) = 1.36, 95% confidence interval (CI) 1.14-1.61; FDR = 0.0869). Colocalization supported a shared causal variant between astrocytic TRIM66 expression and TN (PP.H4 = 0.81).
Discussion
Astrocyte-specific regulation of TRIM66 may contribute to TN pathogenesis through neuroinflammatory pathways, offering a cell-type-resolved mechanistic perspective that complements existing models of TN biology.
Conclusion
Genetic evidence suggests a potential role of astrocyte-mediated regulation of TRIM66 in TN susceptibility. Convergent MR and colocalization suggest TRIM66 as a potential cell-type-resolved candidate warranting further functional validation and therapeutic exploration.
BACKGROUND
Osteoarthritis (OA) is a leading cause of chronic pain and disability worldwide, with growing evidence implicating immune dysregulation in its pathogenesis. However, the specific peripheral immune cell populations contributing causally to OA risk remain poorly characterized.
METHODS
We performed a multi-stage two-sample Mendelian randomization (MR) study integrating single-cell cis-expression quantitative trait loci (cis-eQTLs) for 14 peripheral immune cell types from the OneK1K cohort with two independent OA GWAS datasets - the Million Veteran Program for discovery and the UK Biobank for replication and ICD-10-based subtype analyses. Causal inference was strengthened through Bayesian colocalization, Steiger directionality testing, and phenome-wide pleiotropy screening. Gene-level safety profiling and functional annotation were also performed.
RESULTS
Among the eGene-outcome pairs tested, 13 reached false discovery rate significance in discovery. Two were replicated with concordant effect direction: MAN1A2 in CD4+ naïve and central memory T cells and SLC44A4 in NK cells. Bayesian colocalization supported a shared causal variant for MAN1A2 (PP.H4 = 0.96) and SLC44A4 (PP.H4 = 0.81). However, SLC44A4 was excluded due to extensive HLA-related pleiotropy within the major histocompatibility complex region. MAN1A2 showed concordant risk-increasing effects across all five OA subtypes, reaching significance for hip OA, polyarthrosis, and other unspecified arthrosis. Gene-level phenome-wide testing showed that genetic perturbation of MAN1A2 is not associated with detectable adverse phenotypes in population-based exome data, and functional analysis positioned MAN1A2 within N-glycan processing and endoplasmic reticulum quality control pathways.
CONCLUSION
Cell-type-specific MR identifies MAN1A2 expression in CD4+ naïve T cells as a candidate therapeutic target for osteoarthritis for which genetic perturbation is not associated with detectable adverse phenotypes in population-based exome data.
Xuanyi Zhou, Fangyu Liu, Yan Zhang et al.· Experimental Gerontology· 0 citations
NRXN1 haploinsufficiency is associated with coordinated downregulation of RNA-processing genes in cortical organoids, and the convergence on mRNA nuclear export and RNA-processing genes should be interpreted cautiously and verified by direct experimental perturbation.
Xi Lai, Jing Wen· Progress in Neuro-psychophar...· 0 citations
Study of human-induced pluripotent stem cell derived ventral telencephalic interneuron progenitors in two-dimensional culture finds that transcript level variation is significantly greater between 16p11.2 heterozygous progenitors than their isogenic wild type counterparts, suggesting that the 16p11.2 locus itself has a genome-wide property in stabilizing transcription between cells.
Yifei Yang, Idoia Quintana Urzainqui, T. Pratt· Frontiers in Molecular Neuro...· 0 citations
Background Microglia drive neuroinflammation in Alzheimer’s disease (AD), yet no approved therapy targets this compartment. Human genome-wide association studies consistently implicate innate immune loci in AD risk, establishing microglial transcriptional programs as therapeutically relevant but pharmacologically underexploited targets. Objective We sought to identify transcription factors (TFs) governing microglial state transitions computationally and to nominate structurally tractable drug repurposing candidates. Methods We applied trajectory inference (PAGA), pseudobulk DESeq2, pySCENIC gene regulatory network (GRN) inference, CellChat, and virtual screening of 1,962 approved compounds to 236,002 microglial nuclei from 84 donors (SEA-AD atlas). Results IKZF1 was the sole target TF retained under cisTarget v10 motif constraints, with peak regulon activity in LateAD-DAM (pseudotime ρ = +0.309) and replication in an independent bulk cohort (GSE95587; adjusted P value =.004). CellChat identified SLIT2→ROBO2 from multiple neuron subtypes (predominantly inhibitory interneurons) as the top predicted pathway to microglia. Tafamidis (→IRF8) and diflunisal (→PPARG) were top virtual screening hits; all evaluated compounds failed the pre-specified selectivity threshold. Conclusions IKZF1 is prioritised as a candidate late-disease microglial TF, supported by six convergent evidence dimensions including independent bulk replication. Tafamidis and diflunisal are low-confidence repurposing hypotheses requiring experimental validation.
Background Intervertebral disc degeneration (IVDD) is a common cause of chronic low back pain, imposing a significant economic and physiological burden on individuals and society worldwide. Although dysregulation of the WNT/β-catenin pathway is considered an important factor contributing to the dysfunction of nucleus pulposus (NP) cells and degradation of the extracellular matrix, the mechanisms by which specific subgroups of NP cells are activated and the maintenance of excessive activation of specific pathways remain unclear. Methods We combined single-cell RNA sequencing and spatial transcriptomics with human disc specimens, a rat tail-compression model using static 1.5 MPa loading, an independent rat needle-puncture time-course model, primary NP-cell experiments using continuous static hydrostatic pressure (0.2 MPa for 24 h), WNT-pathway perturbation, molecular docking and dynamics, and targeted siRNA. Computational analyses were interpreted at the cell/spot level, whereas animal-level inference used the stated biological replicates. Results Single-cell transcriptomics identified R-spondin 2 (RSPO2) as a selective marker of a homeostatic NP-resident Cluster 1 compartment whose proportion contracted after mechanical injury, while RSPO2-related WNT/FN1–CD44 signalling scores increased across expanded degenerative effector populations. Human panels were used as representative cross-sectional comparisons without inferential between-grade testing. In NP cells, 0.2 MPa pressure and exogenous RSPO2 enhanced WNT/β-catenin, FN1–CD44, matrix-catabolic and apoptotic responses; IWR-1 and DKK1 attenuated these changes. Molecular docking, 100-ns dynamics and a forward co-immunoprecipitation were consistent with an RSPO2–LGR4 association. RSPO2 worsened degeneration in the 1.5 MPa rat compression model, whereas combined IWR-1 treatment was protective. Spatial transcriptomics provided descriptive maps across the needle-puncture time course, and machine-learning models showed internal spot-level discrimination of the prespecified RSPO2-associated labels. Conclusion RSPO2 is a candidate regulator, rather than only a marker, of an IVDD-associated NP state. The perturbation data support an RSPO2-associated WNT amplification program coupled to FN1–CD44/MMP3 activation, but the proposed ordering remains provisional pending independent-siRNA and rescue validation. The translational potential of this article This study identifies an RSPO2-associated NP state and a candidate WNT/FN1–CD44 programme linked to IVDD. The findings provide a testable basis for future WNT-directed intervention studies while recognising the limits of acute rat models and cross-species data.
Qiu-Wei Li, Guoyan Liang, Kaida Bo et al.· Journal of Orthopaedic Trans...· 0 citations
BACKGROUND
Migraine is a common and disabling neurological disorder, yet most causal regulatory variants and their target cell types remain unresolved. Disease-associated variants are enriched in non-coding cis-regulatory elements, indicating that they act by modulating gene regulation. Chromatin accessibility quantitative trait loci (caQTLs) capture genetic effects on these regulatory elements with cell-type resolution and can pinpoint the regulatory regions and cellular contexts mediating disease risk. However, brain cell type-specific caQTLs have not previously been integrated with migraine genetics.
METHODS
We performed two-sample Mendelian randomization (MR) using brain cell type-specific cis-caQTLs from sorted neuronal (NeuN⁺) and non-neuronal (NeuN⁻) nuclei of 616 postmortem brain donors as exposures, with FinnGen Release 12 migraine GWAS (26,894 cases / 374,605 controls) as the discovery outcome. Open chromatin regions (OCRs) reaching Bonferroni-corrected significance were replicated in the UK Biobank (25,393 cases / 433,047 controls) and the Million Veteran Program (31,836 cases / 405,831 controls), and further evaluated by Bayesian colocalization and instrument-level phenome-wide screening. Multi-modal target gene annotation integrated Hi-C, cis-eQTL, ABC, and ENCODE-rE2G models; nominated genes were further evaluated for drug-target safety using gene-level rare-variant collapsing analyses and characterized for regional brain expression using the Human Protein Atlas.
RESULTS
Of 15,334 OCR-migraine causal estimates, 19 reached Bonferroni-corrected significance in FinnGen R12. Seven were Bonferroni-replicated in both replication cohorts with concordant directions, and three showed strong colocalization (PP.H4 > 0.80). After excluding one OCR with extensive cardiovascular pleiotropy, two non-neuronal OCRs were retained: Peak_7234 (chr1:115,282,554-115,283,246) and Peak_124742 (chr4:35,524,861-35,526,079). Multi-modal annotation of Peak_7234 convergently nominated NGF as the highest-priority candidate target gene, with TSPAN2 as a secondary candidate; Peak_124742 lies in a gene-poor region with insufficient regulatory annotation to confidently nominate a target gene. Neither NGF nor TSPAN2 showed associations reaching phenome-wide significance.
CONCLUSIONS
Two non-neuronal brain open chromatin regions are prioritized as likely causal contributors to migraine risk. At the chr1:115.3 Mb region, NGF is nominated as the highest-priority candidate downstream target, with TSPAN2 as a complementary candidate. These findings extend cell type-specific causal mapping of migraine to the regulatory layer and identify candidate regulatory elements and target genes for further mechanistic and translational investigation.
CLINICAL TRIAL NUMBER
Not applicable.
Qiuhan Xu, Zhaohui Chai, Yu-Ning Zhang et al.· The Journal of Headache and...· 0 citations
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