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In-depth transcriptomic analyses investigating molecular mechanisms underlying diabetic retinopathy (totalRNA)

ABSTRACT: Diabetic Retinopathy (DR) is among the major global causes for vision loss. With the rise in diabetes prevalence, an increase in DR incidence is expected. Current understanding of both the molecular etiology and pathways involved in the initiation and progression of DR is limited. Here we analyzed mRNA and miRNA expression profiles of 80 human post-mortem retinal samples from 80 patients diagnosed with various stages of DR. We found differentially expressed transcripts to be predominantly associated with late stage DR and pathways such as hippo and gap junction signaling. A multivariate regression model identified transcripts with progressive changes throughout disease stages, which in turn displayed significant overlap with sphingolipid and cGMP−PKG signaling. Combined analysis of miRNA and mRNA expression further uncovered disease-relevant miRNA/mRNA associations as potential mechanisms of post-transcriptional regulation. Finally, integrating human retinal single cell RNA-Sequencing data revealed a continuous loss of retinal ganglion cells, and Müller cell mediated changes in histidine and β-alanine signaling. Our findings offer an unprecedented insight into the development of DR and provide potential avenues for future therapeutic intervention.

ORGANISM(S): Homo sapiens

PROVIDER: GSE160306 | GEO | 2021/04/19

REPOSITORIES: GEO

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In-depth transcriptomic analyses investigating molecular mechanisms underlying diabetic retinopathy (smallRNA)

Project description:Diabetic Retinopathy (DR) is among the major global causes for vision loss. With the rise in diabetes prevalence, an increase in DR incidence is expected. Current understanding of both the molecular etiology and pathways involved in the initiation and progression of DR is limited. Here we analyzed mRNA and miRNA expression profiles of 80 human post-mortem retinal samples from 80 patients diagnosed with various stages of DR. We found differentially expressed transcripts to be predominantly associated with late stage DR and pathways such as hippo and gap junction signaling. A multivariate regression model identified transcripts with progressive changes throughout disease stages, which in turn displayed significant overlap with sphingolipid and cGMP−PKG signaling. Combined analysis of miRNA and mRNA expression further uncovered disease-relevant miRNA/mRNA associations as potential mechanisms of post-transcriptional regulation. Finally, integrating human retinal single cell RNA-Sequencing data revealed a continuous loss of retinal ganglion cells, and Müller cell mediated changes in histidine and β-alanine signaling. Our findings offer an unprecedented insight into the development of DR and provide potential avenues for future therapeutic intervention.

2021-04-19 | GSE160308 | GEO

Identification of plant PKG in GA signaling via fine-tuning GAMYB nuclear localization

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Plasmodium PKG interacts with ICM1, a multi-pass membrane protein, in both asexual and sexual stages

2021-02-10 | PXD020447 | Pride

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A multipass membrane protein interacts with the cGMP-dependent protein kinase to regulate critical calcium signals in malaria parasites

Project description:In malaria parasites, all cGMP-dependent signalling is mediated through a single cGMP-dependent protein kinase (PKG). A major function of PKG is to control calcium signals essential for the parasite to exit red blood cells or for transmission to the mosquito vector. However, how PKG controls these signals in the absence of known second messenger-dependent calcium channels or scaffolding proteins remains a mystery. Here we identify a tightly-associated PKG partner protein in both Plasmodium falciparum asexual blood stages and P. berghei gametocytes. Named ICM1, the partner is a polytopic membrane protein with homology to transporters and calcium channels, raising the possibility of a direct functional link between PKG and calcium homeostasis. Phosphoproteomic analyses in both Plasmodium species highlight a densely phosphorylated region of ICM1 with multiple phosphorylation events dependent upon PKG activity. Stage-specific depletion of ICM1 in P. berghei blocks gametogenesis due to the inability of mutant parasites to mobilise intracellular calcium upon PKG activation, whilst conditional disruption of P. falciparum ICM1 results in reduced cGMP-dependent calcium mobilisation associated with defective egress and invasion. Our findings provide new insights into the atypical calcium homeostasis in malaria parasites essential for pathology and disease transmission.

2021-02-10 | PXD020381 | Pride

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A G-protein-coupled receptor modulates gametogenesis via PKG-mediated signaling cascade in Plasmodium berghei

Project description:Gametogenesis is essential for malaria parasite transmission, but the molecular mechanism of this process remains to be refined. Here, we identified a G-protein-coupled receptor 180 (GPR180) that plays a critical role in signal transduction during gametogenesis in Plasmodium. In the rodent parasite P. berghei, PbGPR180 was expressed during asexual and sexual development, with more prominent expression in gametocytes and ookinetes. While PbGPR180 was predominantly localized to cytoplasmic puncta in asexual stages and gametocytes, it became associated with the plasma membrane in female gametes and ookinetes. Knockout of pbgpr180 (Δpbgpr180) had no noticeable effect on asexual development or gametocytogenesis but impaired gamete formation and reduced transmission of the parasites to mosquitoes. Transcriptome analysis of the Δpbgpr180 gametocytes revealed a large proportion of the dysregulated genes with assigned functions in cyclic nucleotide signaling transduction, especially the cGMP-PKG-Ca2+ signaling cascade. Deletion of pbgpr180 resulted in a delay and reduction in cytosolic Ca2+ mobilization during the induction of gametogenesis. In addition, the intracellular cGMP level was significantly reduced in the Δpbgpr180 gametocytes, suggesting that PbGPR180 functions upstream of the cGMP-PKG-Ca2+ signaling pathway. In line with this function, PbGPR180 protein was found to interact with several transmembrane transporter proteins and a small GTPase, Rab6, in activated gametocytes. Allele replacement of pbgpr180 with the P. vivax ortholog pvgpr180 showed equal competence of the transgenic parasite in sexual development, suggesting functional conservation of this gene in Plasmodium spp . These results indicate that GPR180 is involved in cGMP-PKG-Ca2+ signal transduction to regulate gametogenesis in malaria parasites.

2022-04-01 | PXD030837 | Pride

A Protein Kinase G -interacting protein regulates critical calcium signals in malaria parasites (Co-IP)

Project description:In malaria parasites, cGMP signalling is mediated by a single cGMP-dependent protein kinase (PKG) . One of the major functions of PKG is to control calcium signals essential for the parasite to exit red blood cells or for the transmission of the gametocyte stages to the mosquito . However, how PKG controls these signals in the absence of known second messenger-dependent calcium channels or scaffolding proteins remains a mystery. Here we use pull-down approaches to identify a PKG partner protein in both Plasmodium falciparum schizonts and P. berghei gametocytes. This partner, named ICM1, is a polytopic membrane protein with homologies to transporters and calcium channels, raising the possibility of a direct functional link between PKG and calcium homeostasis. Phosphoproteomic analyses in both Plasmodium species highlight a densely phosphorylated region of ICM1 with multiple phosphorylation events dependent on PKG activity. Conditional disruption of the P. falciparum ICM1 gene results in reduced cGMP-dependent calcium mobilisation associated with defective egress and invasion. Stage-specific depletion of ICM1 in P. berghei gametocytes blocks gametogenesis due to the inability of mutant parasites to mobilise intracellular calcium upon PKG activation. These results provide us with new insights into the atypical calcium homeostasis in malaria parasites.

2021-01-25 | PXD020210 | Pride

A Protein Kinase G-interacting protein regulates critical calcium signals in malaria parasites (phosphoproteomic)

Project description:In malaria parasites, cGMP signalling is mediated by a single cGMP-dependent protein kinase (PKG). One of the major functions of PKG is to control calcium signals essential for the parasite to exit red blood cells or for the transmission of the gametocyte stages to the mosquito. However, how PKG controls these signals in the absence of known second messenger-dependent calcium channels or scaffolding proteins remains a mystery. Here we use pull-down approaches to identify a PKG partner protein in both Plasmodium falciparum schizonts and P. berghei gametocytes. This partner, named ICM1, is a polytopic membrane protein with homologies to transporters and calcium channels, raising the possibility of a direct functional link between PKG and calcium homeostasis. Phosphoproteomic analyses in both Plasmodium species highlight a densely phosphorylated region of ICM1 with multiple phosphorylation events dependent on PKG activity. Conditional disruption of the P. falciparum ICM1 gene results in reduced cGMP-dependent calcium mobilisation associated with defective egress and invasion. Stage-specific depletion of ICM1 in P. berghei gametocytes blocks gametogenesis due to the inability of mutant parasites to mobilise intracellular calcium upon PKG activation. These results provide us with new insights into the atypical calcium homeostasis in malaria parasites

2021-01-25 | PXD020189 | Pride

Comparison of gene expression profiles in hearts exposed to pressure overload (PO) with or without sildenafil treatment in PERK wild type (flx) or PERK cardiac-specific knockout 8cko) mice.

Project description:Recently, it is reported that sildenafil suppresses maturation of PO-induced miRNAs. However, the mechanism of how sildenafil coupled NO-cGMP-PKG signaling affects this maturation was not unraveled. Here, we show that PERK-mediated suppression of miRNAs by sildenafil is vital to keep mitochondrial homeostasis, using cardiac-specific PERK knockout (cko) mice.

2020-07-10 | GSE154081 | GEO

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