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Risk Variants for Exfoliation Syndrome Modulate Antisense Promoter Activity Within the LOXL1 Locus

ABSTRACT: The goal of this study was to identify functional variants that play a role in exfoliation syndrome (XFS) pathogenesis. We sequenced the entire LOXL1 locus in 50 South African XFS cases and 50 matched controls. The most strongly associated variants in this dataset were found in a ~7kb region spanning the LOXL1 exon 1/intron 1 boundary. DNase hypersensitivity analysis was used to demonstrate that this region, which lies upstream of the LOXL1 antisense RNA (LOXL1-AS1), contains regulatory activity.

ORGANISM(S): Homo sapiens

PROVIDER: GSE66877 | GEO | 2015/07/22

SECONDARY ACCESSION(S): PRJNA278153

REPOSITORIES: GEO

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Risk Variants for Exfoliation Syndrome Modulate Antisense Promoter Activity Within the LOXL1 Locus

Project description:The goal of this study was to identify functional variants that play a role in exfoliation syndrome (XFS) pathogenesis. We sequenced the entire LOXL1 locus in 50 South African XFS cases and 50 matched controls. The most strongly associated variants in this dataset were found in a ~7kb region spanning the LOXL1 exon 1/intron 1 boundary. DNase hypersensitivity analysis was used to demonstrate that this region, which lies upstream of the LOXL1 antisense RNA (LOXL1-AS1), contains regulatory activity. determining of chromatin structural changes in 3 cell types.

2015-07-22 | E-GEOD-66877 | biostudies-arrayexpress

Roles of LOX and LOXL1 on the transcriptome of hepatic stellate cells

Project description:Our previous studies have found that LOX and LOXL1 were highly upregulated in advanced liver fibrosis; herein, we aimed to investigate the roles of LOX and LOXL1 in hepatic stellate cells.

2021-12-01 | GSE155651 | GEO

Homo sapiens

Project description:Risk Variants for Exfoliation Syndrome Modulate Antisense Promoter Activity Within the LOXL1 Locus

| PRJNA278153 | ENA

Intraductal Xenografts Model Lobular Carcinoma of the Breast and Reveal Matrix Remodeling by LOXL1 as a Targetable Hallmark II

Project description:Invasive lobular carcinoma (ILC) is the most frequent specific histological subtype of breast cancer (BC). It has distinct clinical features from other estrogen receptor positive (ER+) BCs but the molecular mechanisms underlying the characteristic biology are unclear because we lack experimental models to study it. Here, we generate xenograft models with ILC-derived SUM-44 PE and MDA-MB-134-VI cells by grafting them to mouse milk ducts that recapitulate the human disease including metastasis to visceral organs. Transcriptomic analysis of intraductal ER+ PDXs reveals extracellular matrix modulation as an ILC-specific trait. This signature confirms in patient datasets. The collagen modifying enzyme LOXL1 is overexpressed specifically in ILCs by tumor cells; treatment with a LOX inhibitor, BAPN, and LOXL1 silencing decrease tumor growth and inhibit metastasis by disrupting ECM structure/fibrils with down modulation of ER, IGFR, and FGFR signaling. Hence inhibition of LOXL1 is a promising therapeutic strategy for ILC.

2020-12-09 | GSE149675 | GEO

Intraductal Xenografts Model Lobular Carcinoma of the Breast and Reveal Matrix Remodeling by LOXL1 as a Targetable Hallmark I

2020-12-09 | GSE149671 | GEO

Exogenous expression of Lox, Loxl1 and Loxl2 regulate gene expression in primary murine lung fibroblasts.

Project description:Primary murine lung fibroblasts were transfected with either control (scrambled) or sequence-specific siRNA against Lysyl oxidase (Lox), Lysyl oxidase-like (Loxl1) or Lysyl oxidase-like 2 (Loxl2) genes. Cells were harvested 48 hours after the transfection. Multiple changes in gene expression were found in the corrected p values in this microarray study.

2016-10-25 | GSE89121 | GEO

NEI Exfoliation Genotyping Study

Project description:The overall goal of our research is to elucidate the pathogenesis of exfoliation syndrome and the associated glaucoma, making it possible to implement effective screening and prevention strategies and to develop novel therapies. Cases genotyped for this project are from the Nurses Health Study (NHS), the Health Professionals Follow-up Study (HPFS), the Women's Genome Health Study (WGHS), the Massachusetts Eye and Ear Infirmary (MEEI), Mayo Clinic, the University of Iowa, the University of Miami and Duke University Medical Center. Exfoliation syndrome (XFS) is a common condition that is a major risk factor for high-tension open-angle glaucoma, pre-mature cataract formation, and increased risk of complications during cataract surgery. Previous studies suggest that exfoliation syndrome and the related glaucoma (XFG) are genetically complex, and one gene, LOXL1, has been identified as a major genetic risk factor. LOXL1 variants are found in up to 98% of affected patients; however, these same variants are also present in up to 80% of unaffected individuals, indicating that additional genetic and/or environmental factors are necessary for disease development. Samples genotyped for this study are a case set (1,096 samples) and 24 pedigrees (98 samples). Controls for association analyses are selected from the NEIGHBORHOOD study.

| phs001053 | dbGaP

Compositional analysis of extracellular aggregates in the eyes of patients with exfoliation syndrome and exfoliation glaucoma.

Project description:Exfoliation syndrome (XFS) is a condition characterized by the production of insoluble fibrillar aggregates (exfoliation material; XFM) in the eye and elsewhere. Many patients with XFS progress to exfoliation glaucoma (XFG), a significant cause of global blindness. We used quantitative mass spectrometry to analyze the composition of XFM in lens capsule specimens and aqueous humor samples from XFS and XFG patients and individuals without XFS. Pieces of lens capsule and samples of aqueous humor were obtained with consent from patients undergoing cataract surgery. Tryptic digests of capsule or aqueous samples were analyzed by HPLC-mass spectrometry and relative differences between samples were quantified using the tandem mass tag technique. The distribution of XFM on the capsular surface was visualized by scanning electron microscopy and super-resolution light microscopy. A small set of proteins was consistently upregulated in XFS samples, including microfibril components fibrillin-1 (FBN1), latent TGFBeta-binding protein-2 (LTBP-2), and LTBP-3. Lysyl oxidase-like 1 (LOXL1), a protein linked strongly to XFS in genetic studies, was an abundant XFM protein. Ligands of the TGFBeta superfamily were prominent, including LEFTY2, a protein known for its role in establishing the embryonic body axis. Elevated levels of LEFTY2 were also detected in aqueous humor from XFG patients and confirmed by ELISA. This analysis verified the presence of several suspected XFM proteins and identified novel components. Quantitative comparisons between patient samples revealed a consistent XFM proteome. The expression of FBN1, LOXL1, and LEFTY2 was particularly strong in XFG patients in comparison to XFS patients.

2022-02-17 | PXD026764 | Pride

Riboseq and Quantseq of neuroblastoma cell line SH-SY5Y expressing MAPT-AS1 constructs

Project description:The aim of this experiment was to assess the on- and off-target effects of MAPT-AS1 expression, and whether mutations/deletions to MAPT-AS1 alter these effects. SHSY5Y cells stably expressing variants of MAPT-AS1 were analyzed by Riboseq and Quantseq.

2021-03-20 | E-MTAB-9921 | biostudies-arrayexpress

Silencing of NFYC-AS1 by Gapmer antisense oligonucleotides and CRISPR/Cas9 TSS deletion.

Project description:NFYC-AS1 is an overlapping antisense RNA transcribed head-to-head to NFYC sense gene, encoding for the subunit C of NF-Y transcription factor, which is known as master regulator of cell cycle and proliferation in normal and tumor cells. Here we performed NFYC-AS1 silencing in lung squamous carcinoma H520 cells by Gapmer antisense oligonucleotides and CRISPR/Cas9 TSS deletion. Afterwards, we performed differentially expressed analysis and gene set enrichement analysis to investigate on NFYC-AS1 function and mechanism of action.

2024-03-08 | GSE240468 | GEO

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