BACKGROUND:Transcriptome-wide association studies (TWAS) identify genetically regulated expression (GReX) components and can pinpoint causal genes in genome-wide association studies but are often limited by a single-cell context. OBJECTIVE:We hypothesized that modeling GReX across multiple conditions could enhance power to identify causal genes for complex inflammatory diseases. METHODS:We conducted TWAS on 400 transcriptomes under 8 proinflammatory cytokine stimulations in keratinocytes, modeling GReX for 18,599 genes against genome-wide association studies from 7 inflammatory skin diseases: atopic dermatitis, psoriasis, acne, alopecia areata, systemic sclerosis, systemic lupus erythematosus, and vitiligo. RESULTS:Our TWAS identified 274 loci from the 7 diseases that harbor a single significant TWAS gene association. We nominated causal genes and their associated proinflammatory cytokine stimuli, including ERAP2 for psoriasis with IL-17A + TNF-α stimulation; WNT10A for acne with IFN-γ stimulation; and RAET1L, MAP3K11, and ITGAM for alopecia areata, acne, and systemic lupus erythematosus, respectively, with TNF stimulation. Notably, our TWAS-identified genes showed overwhelming evidence of colocalization with genome-wide association study signals (P = 1.03 × 10-15), and our method successfully captured >85% of all genes with colocalizing expression quantitative trait loci. Single-cell-resolution spatial profiling further demonstrated the modulation of TWAS signals in keratinocytes by close proximity to TNF/IL-17-expressing cells in psoriatic skin. CONCLUSION:Modeling gene expression across relevant cellular states substantially improves the power and resolution of TWAS.

Gene regulation is intricately influenced by the three-dimensional organization of the genome. In particular, chromatin can exist in loop structures that enable long-range regulatory interactions. By utilizing chromosome conformation capture techniques such as Hi-C, valuable information regarding the organization of these loop structures in 3D space can be obtained. Although functional/feature enrichment is now a common downstream analysis for various genomic platforms to provide biological context, tools specifically designed for high-throughput assays that capture chromosome conformation remain relatively limited. Here, we present Loopsim, a command-line application that performs enrichment analysis on Hi-C loop profiles against user-defined regions (available on GitHub at https://github.com/CutaneousBioinf/Loopsim). Loopsim efficiently simulates a background distribution using a distinctive sampling approach that considers loop size, intervals, loop-loop distances, and structure; it then computes statistics based on the empirical null distribution.

Psoriasis is a common inflammatory skin disease with heterogeneous presentation. Up to 30

Intraocular lacrimal gland choristoma - IJOOO- Print ISSN No: - 2581-5024 Online ISSN No:- 2581-5016 Article DOI No:- 10.18231/j.ijooo.2024.008, IP International Journal of Ocular Oncology and Oculoplasty-IP Int J Ocul Oncol Oculoplasty

Background: Intra-arterial chemotherapy (IAC) is increasingly used in managing patients with retinoblastoma. In Australia, IAC is primarily used as a globe-salvage treatment when primary treatment has failed. Methods: A retrospective, single-institution study conducted on consecutive children treated with IAC at the Royal Children’s Hospital, Victoria, Australia between September 2009 to January 2021. Results: Using the Intraocular Classification of Retinoblastoma (ICRB), 16 eyes of 14 children classified as group A (n=1), Group B (n=3), Group D (n=10), or Group E (n=2) were treated with IAC. All but one child received IAC as secondary treatment for relapsed or refractory disease. Successful catheterisation of the ophthalmic artery was achieved in 37/46 (80.4%) procedures. A systemic complication occurred in one child (n=1): radiological evidence of a watershed infarct. Local complications of IAC included conjunctival injection (n=1), forehead rash (n=1), sixth cranial nerve palsy (n=2), ptosis (n=2), hemi-retinal ischaemia (n=1), choroidal ischaemia (n=1), retinal detachment (n=2), and choroidal neovascularisation (n=1). Regional extra-ocular disease occurred in one child. No child had distant metastatic disease and no child died. The overall globe salvage rate was 8/16 (50%): Group A (n=1, 100%), group B (n=2, 66.6%), Group D (n=5, 50%), group E (n=0, 0%). Kaplan Meier analysis of ocular survival following treatment with IAC was 75%, 68% and 53% for 6 months, 1 year and 2 years, respectively. Conclusions: Our experience demonstrates that IAC can be a useful treatment modality for refractory retinoblastoma in globe salvage, with an acceptable side-effect profile.

Convection-enhanced delivery for central nervous system gene therapy is an emerging treatment strategy to modify the course of previously untreatable or inadequately treated neurologic conditions, including brain tumors, metabolic disorders, epilepsy, and neurodegenerative disorders. Ongoing nervous system gene therapy clinical trials highlight advantages and ongoing challenges to this therapeutic paradigm.

Purpose: To evaluate high-risk histopathological features following primary enucleation of eyes with retinoblastoma and assess the patient outcomes across continents. Methods: A retrospective study of 1,426 primarily enucleated retinoblastoma eyes from five continents. Results: Of all, 923 (65%) were from Asia (AS), 27 (2%) from Australia (AUS), 120 (8%) from Europe (EUR), 162 (11%) from North America (NA), and 194 (14%) from South America (SA). Based on the continent (AS vs. AUS vs. EUR vs. NA vs. SA), the histopathological features included massive choroidal invasion (31% vs. 7% vs. 13% vs. 19% vs. 27%, P = 0.001), postlaminar optic nerve invasion (27% vs. 0% vs. 16% vs. 21% vs. 19%, P = 0.0006), scleral infiltration (5% vs. 0% vs. 4% vs. 2% vs. 7%, P = 0.13), and microscopic extrascleral infiltration (4% vs. 0% vs. <1% vs. <1% vs. 4%, P = 0.68). Adjuvant chemotherapy with/without orbital radiotherapy was given to 761 (53%) patients. Based on Kaplan-Meier estimates in different continents (AS vs. AUS vs. EUR vs. NA vs. SA), the 6-year risk of orbital tumor recurrence was 5% versus 2% versus 0% versus 0% versus 12% (P < 0.001), systemic metastasis was reported in 8% versus 5% versus 2% versus 0% versus 13% (P = 0.001), and death in 10% versus 3% versus 2% versus 0% versus 11% (P < 0.001) patients. Conclusion: There is a wide variation in the infiltrative histopathological features of retinoblastoma across continents, resulting in variable outcomes. SA and AS had a higher risk of orbital tumor recurrence, systemic metastasis, and death compared to AUS, EUR, and NA.

Background/Aims The incidence of retinopathy of prematurity (ROP) is increasing and treatment options are expanding, often without accompanying safety data. We aimed to define a minimal, patient-centred data set that is feasible to collect in clinical practice and can be used collaboratively to track and compare outcomes of ROP treatment with a view to improving patient outcomes. Methods A multinational group of clinicians and a patient representative with expertise in ROP and registry development collaborated to develop a data set that focused on real-world parameters and outcomes that were patient centred, minimal and feasible to collect in routine clinical practice. Results For babies receiving ROP treatment, we recommend patient demographics, systemic comorbidities, ROP status, treatment details, ophthalmic and systemic complications of treatment, ophthalmic and neurodevelopmental outcomes at initial treatment, any episodes of retreatment and follow-up examinations in the short and long-term to be collected for use in ROP studies, registries and routine clinical practice. Conclusions We recommend these parameters to be used in registries and future studies of ROP treatment, to reduce the variation seen in previous reports and allow meaningful assessments and comparisons. They form the basis of the EU-ROP and the Fight Childhood Blindness! ROP Registries.

Long noncoding RNAs (lncRNAs) regulate the expression of protein-coding genes and have been shown to play important roles in inflammatory skin diseases. However, we still have limited understanding of the functional impact of lncRNAs in skin, partly due to their tissue specificity and lower expression levels compared with protein-coding genes. We compiled a comprehensive list of 18,517 lncRNAs from different sources and studied their expression profiles in 834 RNA-Seq samples from multiple inflammatory skin conditions and cytokine-stimulated keratinocytes. Applying a balanced random forest to predict involvement in biological functions, we achieved a median AUROC of 0.79 in 10-fold cross-validation, identifying significant DNA binding domains (DBDs) for 39 lncRNAs. G18244, a skin-expressing lncRNA predicted for IL-4/IL-13 signaling in keratinocytes, was highly correlated in expression with F13A1, a protein-coding gene involved in macrophage regulation, and we further identified a significant DBD in F13A1 for G18244. Reflecting clinical implications, AC090198.1 (predicted for IL-17 pathway) and AC005332.6 (predicted for IFN-γ pathway) had significant negative correlation with the SCORAD metric for atopic dermatitis. We also utilized single-cell RNA and spatial sequencing data to validate cell type specificity. Our research demonstrates lncRNAs have important immunological roles and can help prioritize their impact on inflammatory skin diseases.

BACKGROUNDMultiple treatment options are available for the management of psoriasis, but clinical response varies among individual patients and no biomarkers are available to facilitate treatment selection for improved patient outcomes.OBJECTIVESWe aim to utilize retrospective data to conduct a pharmacogenetic study. This design can bypass the obstacle of patient follow-up in prospective study and increase the sample size. Successful implementation of the study can nominate new candidates and their target genes to explore the potential genetic pathways associated with drug response in the treatment of psoriasis.METHODSWe conducted a retrospective pharmacogenetic study using self-evaluated treatment response from 1,942 genotyped psoriatic patients. We examined 6,502,658 genetic markers to model their associations with responses from six treatment options using linear regression, adjusting for cohort variables and demographic features. We further utilized an integrative approach incorporating epigenomic, transcriptomic, and a longitudinal clinical cohort to provide biological implications for the top signals associated with drug response.RESULTSTwo novel markers were revealed to be associated with treatment response: rs1991820 (p = 1.30×10-6) for anti-TNF biologics; and rs62264137 (p = 2.94×10-6) for methotrexate, which also associated with cutaneous mRNA expression levels of two known psoriasis-related genes KLK7 (p = 1.0×10-12) and CD200 (p = 5.4×10-6). We demonstrate that KLK7 expression is increased in the psoriatic epidermis as shown by immunohistochemistry as well as single-cell RNA-sequencing, and we highlight its responsiveness to anti-TNF treatment. By inhibiting the expression of KLK7, we further illustrate keratinocytes have decrease in pro-inflammatory responses to TNF.CONCLUSIONSOur study implicates the genetic regulation of cytokine responses in predicting clinical drug response and supports the association between pharmacogenetic loci and anti-TNF response, as shown here for KLK7.

Psoriasis is an immune-mediated multifactorial genetic disease characterized by cutaneous and joint symptoms ( Boehncke and Schön, 2015 Boehncke W.H. Schön M.P. Psoriasis. Lancet. 2015; 386: 983-994 Abstract Full Text Full Text PDF PubMed Scopus (1690) Google Scholar ). Whereas psoriasis mainly affects the skin and joints, chronic skin inflammation affects metabolic pathways and drives systemic inflammation ( Boehncke, 2018 Boehncke W.H. Systemic inflammation and cardiovascular comorbidity in psoriasis patients: causes and consequences. Front Immunol. 2018; 9: 579 Crossref PubMed Scopus (186) Google Scholar ). Epidemiological studies reported an increased psoriasis risk of several HLA-related diseases ( Boehncke and Schön, 2015 Boehncke W.H. Schön M.P. Psoriasis. Lancet. 2015; 386: 983-994 Abstract Full Text Full Text PDF PubMed Scopus (1690) Google Scholar ). Epidemiological studies reported increased comorbidity of psoriasis with multiple metabolic conditions, such as higher levels of low-density lipoprotein cholesterol and triglycerides ( Botelho et al, 2020 Botelho K.P. Pontes M.A.A. Rodrigues C.E.M. Freitas M.V.C. Prevalence of metabolic syndrome among patients with psoriasis treated with TNF inhibitors and the effects of anti-TNF therapy on their lipid profile: a prospective cohort study. Metab Syndr Relat Disord. 2020; 18: 154-160 Crossref PubMed Scopus (12) Google Scholar ; Ramezani et al, 2019 Ramezani M. Zavattaro E. Sadeghi M. Evaluation of serum lipid, lipoprotein, and apolipoprotein levels in psoriatic patients: a systematic review and meta-analysis of case-control studies. Postepy Dermatol Alergol. 2019; 36: 692-702 Crossref PubMed Scopus (17) Google Scholar ). These findings call for a comprehensive, genome-wide interpretation of the comorbidities between immune-mediated and metabolic traits and psoriasis. With the advent and dissemination of large-scale GWASs, genetic correlation studies have been conducted using GWAS summary statistics ( Kanai et al, 2018 Kanai M. Akiyama M. Takahashi A. Matoba N. Momozawa Y. Ikeda M. et al. Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases. Nat Genet. 2018; 50: 390-400 Crossref PubMed Scopus (429) Google Scholar ). An earlier cross-trait genetic correlation analysis that included psoriasis and performed with SumHer ( Speed and Balding, 2019 Speed D. Balding D.J. SumHer better estimates the SNP heritability of complex traits from summary statistics. Nat Genet. 2019; 51: 277-284 Crossref PubMed Scopus (115) Google Scholar ) revealed a significant association of psoriasis with coronary artery disease and nominal associations with four diseases: type 1 diabetes, type 2 diabetes, ulcerative colitis (UC), and celiac disease. In that study, psoriasis GWAS data from the Wellcome Trust Case Control Consortium 2 were relatively small (7,474 samples). Further genetic correlation analyses between quantitative clinical biomarkers and psoriasis were therefore warranted. None of the findings were replicated with linkage disequilibrium score regression: another popular genetic correlation analysis tool ( Bulik-Sullivan et al., 2015 Bulik-Sullivan B.K. Loh P.R. Finucane H.K. Ripke S. Yang J. Schizophrenia Working Group of the Psychiatric Genomics Consortium et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat Genet. 2015; 47: 291-295 Crossref PubMed Scopus (2194) Google Scholar ). Comprehensive genetic correlation analyses between quantitative clinical biomarkers and psoriasis were therefore warranted.

Hereditary congenital facial paresis type 1 (HCFP1) is an autosomal dominant disorder of absent or limited facial movement that maps to chromosome 3q21-q22 and is hypothesized to result from facial branchial motor neuron (FBMN) maldevelopment. In the present study, we report that HCFP1 results from heterozygous duplications within a neuron-specific GATA2 regulatory region that includes two enhancers and one silencer, and from noncoding single-nucleotide variants (SNVs) within the silencer. Some SNVs impair binding of NR2F1 to the silencer in vitro and in vivo and attenuate in vivo enhancer reporter expression in FBMNs. Gata2 and its effector Gata3 are essential for inner-ear efferent neuron (IEE) but not FBMN development. A humanized HCFP1 mouse model extends Gata2 expression, favors the formation of IEEs over FBMNs and is rescued by conditional loss of Gata3 . These findings highlight the importance of temporal gene regulation in development and of noncoding variation in rare mendelian disease.

Background Observational research suggests that vitamin D levels affect psoriasis. However, observational studies are prone to potential confounding or reverse causation, which complicates interpreting the data and drawing causal conclusions.Aim To apply Mendelian randomization (MR) methods to comprehensively assess a potential association between vitamin D and psoriasis.Methods Genetic variants strongly associated with 25-hydroxyvitamin D (25OHD) in genome-wide association study (GWAS) data from 417 580 and 79 366 individuals from two independent studies served as instrumental variables (used as the discovery and replication datasets, respectively). As the outcome variable, we used GWAS data of psoriasis (13 229 people in the case group, 21 543 in the control group). We used (i) biologically validated genetic instruments, and (ii) polygenic genetic instruments to assess the relationship between genetically proxied vitamin D and psoriasis. We carried out inverse-variance weighted (IVW) MR analyses for the primary analysis. In sensitivity analyses, we used robust MR approaches.Results MR analyses of both the discovery and replication datasets did not show an effect of 25OHD on psoriasis. Neither the IVW MR analysis of the biologically validated instruments [discovery dataset: odds ratio (OR) 0.99; 95% confidence interval (CI) 0.88-1.12, P = 0.873; replication dataset: OR 0.98, 95% CI 0.66-1.46, P = 0.930] nor that of the polygenic genetic instruments (discovery dataset: OR 1.00, 95% CI 0.81-1.22, P = 0.973; replication dataset: OR 0.94, 95% CI 0.64-1.38, P = 0.737) revealed an impact of 25OHD on psoriasis.Conclusion The present MR study did not support the hypothesis that vitamin D levels, measured by 25OHD, affect psoriasis. This study was conducted on Europeans, so the conclusions may not be applicable to all ethnicities.

The immunopathogenesis of psoriasis, a common chronic inflammatory disease of the skin, is incompletely understood. Here we demonstrate, using a combination of single cell and spatial RNA sequencing, IL-36 dependent amplification of IL-17A and TNF inflammatory responses in the absence of neutrophil proteases, which primarily occur within the supraspinous layer of the psoriatic epidermis. We further show that a subset of SFRP2+ fibroblasts in psoriasis contribute to amplification of the immune network through transition to a pro-inflammatory state. The SFRP2+ fibroblast communication network involves production of CCL13, CCL19 and CXCL12, connected by ligand-receptor interactions to other spatially proximate cell types: CCR2+ myeloid cells, CCR7+ LAMP3+ dendritic cells, and CXCR4 expressed on both CD8+ Tc17 cells and keratinocytes, respectively. The SFRP2+ fibroblasts also express cathepsin S, further amplifying inflammatory responses by activating IL-36G in keratinocytes. These data provide an in-depth view of psoriasis pathogenesis, which expands our understanding of the critical cellular participants to include inflammatory fibroblasts and their cellular interactions.

T-cells undergo polyclonal expansion in cutaneous psoriasis (PsC) and PsA, with persistence of "driver clones" after effective treatment (JCI 127:4031; JI 172:1935). A recent scRNA-seq study found roughly equal compartments of clonal and non-clonal Th17 and Tc17 cells in PsC (Science 371:364). We and others have shown that Th17 expansion from PBMC requires contact between monocytes and memory T-cells in the context of TCR ligation (PNAS 104:17034; SID 139:1245). We stimulated PBMC (n=153) with anti-CD3/CD28 beads for 0 or 24h followed by flow cytometry (CD3+CD45RO+,CD4/CD8,CLA+/CLA-). Activation-related DEGs featured marked up-regulation of Th17 signature mRNAs (IL17A, IL17F, IL22, and CCL22) along with the Th1 cytokine IFNG, with a corresponding induction of IL-17A and IL-22 proteins by flow cytometry. These findings were confirmed by cluster analysis of scRNA-seq libraries of CD3/CD28-activated PBMC (n=4 subjects). Stratified analysis of skin homing in CD3/CD28-activated cells revealed 2.9 to 12.1-fold upregulation of IL17A, IL17F, IL22, and CCL22 in CLA+ vs CLA-, without a corresponding difference in IFNG. IL17A and IL17F were overexpressed in activated T-cells from psoriatics vs. controls (each 1.9-fold, p=4.7x10-4). As revealed by scRNA-seq of lesional psoriatic skin, IL17A was overexpressed (2.2-fold, p= 0.003) in skin-homing (FUT7+) vs non-skin-homing (FUT7-) T-cells, whereas IFNG was not. As reported in a recent CITE-seq study (Front Immunol 12:636720), our bulk- and sc-RNA-seq experiments revealed dramatic disappearance of monocytes within 24h of CD3/CD28 activation, which was confirmed by imaging flow cytometry and morphologically identified as apoptosis by time-lapse microscopy. Taken together with data showing IL-23 expression by inflammatory monocyte-like cells in dermal clusters in PsC (JID 141:1707), our experiments suggest a contact-dependent interplay between activated T-cells and monocyte-derived cells in dermal clusters, which maintains polyclonal activation of skin-homing Th17 cells in psoriatic lesions

When enhancer regions are transcribed, stimulus and cell type-dependent non-coding enhancer RNAs (eRNAs) are generated. Recent work suggests eRNAs are not just transcriptional by-products of active enhancers, but have a direct role in gene regulation, yet the role of eRNA in keratinocytes (KC) remains to be elaborated. Since the dynamic transcription of eRNAs makes it difficult to sufficiently capture their expression at steady state, we measured nascent RNAs using Bru-seq. Three replicates each of immortalized KC (N/TERT-2G) were left unstimulated or stimulated with IL-17A+TNF or IL-13 for 30 or 120 min. Focusing on 122,215 accessible ATAC-seq peaks from a total of 20 cytokine-stimulated or unstimulated KC, we found 67,489 (55%) expressed in Bru-seq (≥1 read per sample on average). Excluding 10,166 peaks (15%) in proximity (±500bp) to known promoter regions, we calculated the enrichment of pcHiC loops in three stimulated and unstimulated KC samples. Bru-seq expressed peaks overlapped putative enhancers from pcHiC more often than expected in random simulation (p≤1.8x10-276, FC≥1.6). We then conducted differential expression (DE) between stimulated and unstimulated Bru-seq, after normalizing and adjusting for batch effect. With 30 minutes of IL-13 stimulation, 27 peaks were DE, rising to 157 with 120 minutes, while for IL-17A+TNF, there were 480 and 522 DE peaks, respectively. Compared with ATAC peaks without Bru-seq reads, DE peaks were even more enriched for pcHiC loops (p≤9.8x10-43, FC≥2.7), highlighting context-specific deployment of enhancers. Loops connecting the eRNAs to promoters were found for 369 protein-coding genes, of which 64 were present in all three pcHiC samples, including TNFAIP3 and IL1A (up-regulated with both 30 and 120 minutes of IL-17A+TNF stimulation), TMPRSS11F (down-regulated with 120 minutes of IL-13 stimulation) and IL6 (up-regulated with 30 but not 120 minutes of IL-17A+TNF stimulation). Thus, eRNAs profiled by Bru-Seq can provide unprecedented information in understanding enhancer-mediated gene regulation in keratinocytes.