Bulk Gene Expression Deconvolution Reveals Infiltration of M2 Macrophages in Retinal Neovascularization

IC100, a humanized therapeutic monoclonal anti-ASC antibody alleviates oxygen-induced retinopathy in mice

BACKGROUND

Retinopathy of prematurity (ROP), which often presents with bronchopulmonary dysplasia (BPD), is among the most common morbidities affecting extremely premature infants and is a leading cause of severe vision impairment in children worldwide. Activations of the inflammasome cascade and microglia have been implicated in playing a role in the development of both ROP and BPD. Apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) is pivotal in inflammasome assembly. Utilizing mouse models of both oxygen-induced retinopathy (OIR) and BPD, this study was designed to test the hypothesis that hyperoxia induces ASC speck formation, which leads to microglial activation and retinopathy, and that inhibition of ASC speck formation by a humanized monoclonal antibody, IC100, directed against ASC, will ameliorate microglial activation and abnormal retinal vascular formation.

METHODS

We first tested ASC speck formation in the retina of ASC-citrine reporter mice expressing ASC fusion protein with a C-terminal citrine (fluorescent GFP isoform) using a BPD model that causes both lung and eye injury by exposing newborn mice to room air (RA) or 85% O2 from postnatal day (P) 1 to P14. The retinas were dissected on P14 and retinal flat mounts were used to detect vascular endothelium with AF-594-conjugated isolectin B4 (IB4) and citrine-tagged ASC specks. To assess the effects of IC100 on an OIR model, newborn ASC citrine reporter mice and wildtype mice (C57BL/6 J) were exposed to RA from P1 to P6, then 75% O2 from P7 to P11, and then to RA from P12 to P18. At P12 mice were randomized to the following groups: RA with placebo PBS (RA-PBS), O2 with PBS (O2-PBS), O2 + IC100 intravitreal injection (O2-IC100-IVT), and O2 + IC100 intraperitoneal injection (O2-IC100-IP). Retinal vascularization was evaluated by flat mount staining with IB4. Microglial activation was detected by immunofluorescence staining for allograft inflammatory factor 1 (AIF-1) and CD206. Retinal structure was analyzed on H&E-stained sections, and function was analyzed by pattern electroretinography (PERG). RNA-sequencing (RNA-seq) of the retinas was performed to determine the transcriptional effects of IC100 treatment in OIR.

RESULTS

ASC specks were significantly increased in the retinas by hyperoxia exposure and colocalized with the abnormal vasculature in both BPD and OIR models, and this was associated with increased microglial activation. Treatment with IC100-IVT or IC100-IP significantly reduced vaso-obliteration and intravitreal neovascularization. IC100-IVT treatment also reduced retinal microglial activation, restored retinal structure, and improved retinal function. RNA-seq showed that IC100 treatment corrected the induction of genes associated with angiogenesis, leukocyte migration, and VEGF signaling caused by O2. IC100 also corrected the suppression of genes associated with cell junction assembly, neuron projection, and neuron recognition caused by O2.

CONCLUSION

These data demonstrate the crucial role of ASC in the pathogenesis of OIR and the efficacy of a humanized therapeutic anti-ASC antibody in treating OIR mice. Thus, this anti-ASC antibody may potentially be considered in diseases associated with oxygen stresses and retinopathy, such as ROP.

Upregulation of HMOX1 associated with M2 macrophage infiltration and ferroptosis in proliferative diabetic retinopathy

The roles of immune cell infiltration and ferroptosis in the progression of proliferative diabetic retinopathy (PDR) remain unclear. To identify upregulated molecules associated with immune infiltration and ferroptosis in PDR, GSE60436 and GSE102485 datasets were downloaded from the Gene Expression Omnibus (GEO). Genes associated with immune cell infiltration were examined through Weighted Gene Co-expression Network Analysis (WGCNA) and CIBERSORT algorithm. Common differentially expressed genes (DEGs) were intersected with ferroptosis-associated and immune cell infiltration-related genes. Localization of cellular expression was confirmed by single-cell analysis of GSE165784 dataset. Findings were validated by qRT-PCR, ELISA, Western blotting, and immunofluorescence staining. As a result, the infiltration of M2 macrophages was significantly elevated in fibrovascular membrane samples from PDR patients than the retinas of control subjects. Analysis of DEGs, M2 macrophage-related genes and ferroptosis-related genes identified three hub intersecting genes, TP53, HMOX1 and PPARA. qRT-PCR showed that HMOX1 was significantly higher in the oxygen-induced retinopathy (OIR) mouse model retinas than in controls. Single-cell analysis confirmed that HMOX1 was located in M2 macrophages. ELISA and western blotting revealed elevated levels of HMOX1 in the vitreous humor of PDR patients and OIR retinas, and immunofluorescence staining showed that HMOX1 co-localized with M2 macrophages in the retinas of OIR mice. This study offers novel insights into the mechanisms associated with immune cell infiltration and ferroptosis in PDR. HMOX1 expression correlated with M2 macrophage infiltration and ferroptosis, which may play a crucial role in PDR pathogenesis.

Role of macrophage in ocular neovascularization

Ocular neovascularization is the leading cause of blindness in clinical settings. Pathological angiogenesis of the eye can be divided into corneal neovascularization (CoNV), retinal neovascularization (RNV, including diabetic retinopathy and retinopathy of prematurity), and choroidal neovascularization (CNV) based on the anatomical location of abnormal neovascularization. Although anti-Vascular endothelial growth factor (VEGF) agents have wide-ranging clinical applications and are an effective treatment for neovascular eye disease, many deficiencies in this treatment strategy remain. Recently, emerging evidence has demonstrated that macrophages are vital during the process of physiological and pathological angiogenesis. Monocyte-macrophage lineage is diverse and plastic, they can shift between different activation modes and have different functions. Due to the obvious regulatory effect of macrophages on inflammation and angiogenesis, macrophages have been increasingly studied in the field of ophthalmology. Here, we detail how macrophage activated and the role of different subtypes of macrophages in the pathogenesis of ocular neovascularization. The complexity of macrophages has recently taken center stage owing to their subset diversity and tightly regulated molecular and metabolic phenotypes. In this review, we reveal the functional and phenotypic characterization of macrophage subsets associated with ocular neovascularization, more in-depth research is needed to explore the specific mechanisms by which macrophages regulate angiogenesis as well as macrophage polarization. Targeted regulation of macrophage differentiation based on their phenotype and function could be an effective approach to treat and manage ocular neovascularization in the future.

Comprehensive exploration of hub genes involved in oxidative stress in rhegmatogenous retinal detachment based on bioinformatics analysis

Rhegmatogenous retinal detachment (RRD) is a type of ophthalmologic emergency, if left untreated, the blindness rate approaches 100 %. The RRD patient postoperative recovery of visual function is unsatisfactory, most notably due to photoreceptor death. We conducted to identify the key genes for oxidative stress (OS) in RRD through bioinformatics analysis and clinical validation, thus providing new ideas for the recovery of visual function in RRD patients after surgery. A gene database for RRD was obtained from the Gene Expression Omnibus (GEO) database (GSE28133). Then we screened differentially expressed OS genes (DEOSGs) from the database and assessed the critical pathways in RRD with Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Protein-protein interaction (PPI) networks and hub genes among the common DEOSGs were identified. In addition, we collected general information and vitreous fluid from 42 patients with RRD and 22 controls [11 each of epiretinal membrane (EM) and macular hole (MH)], examined the expression levels of proteins encoded by hub genes in vitreous fluid by enzyme-linked immunosorbent assay (ELISA) to further assess the relationship between the ELISA data and the clinical characteristics of patients with RRD. Ten hub genes (CCL2, ICAM1, STAT3, CD4, ITGAM, PTPRC, CCL5, IL18, TLR2, VCAM1) were finally screened out from the dataset. The ELISA results showed that, compared with the control group, patients with RRD: TLR2 and ICAM-1 were significantly elevated, and CCL2 had a tendency to be elevated, but no statistically significant; RRD patients and MH patients compared with EM patients: STAT3 and VCAM-1 were significantly elevated. We found affected eyes of RRD patients compared with healthy eyes: temporal and nasal retinal nerve fiber layer (RNFL) were significantly thickened. By correlation analysis, we found that: STAT3 was negatively correlated with ocular perfusion pressure (OPP); temporal RNFL was not only significantly positively correlated with CCL2, but also negatively correlated with Scotopic b-wave amplitude. These findings help us to further explore the mechanism of RRD development and provide new ideas for finding postoperative visual function recovery.

Rat Deconvolution as Knowledge Miner for Immune Cell Trafficking from Toxicogenomics Databases

Toxicogenomics databases are useful for understanding biological responses in individuals because they include a diverse spectrum of biological responses. Although these databases contain no information regarding immune cells in the liver, which are important in the progression of liver injury, deconvolution that estimates cell-type proportions from bulk transcriptome could extend immune information. However, deconvolution has been mainly applied to humans and mice and less often to rats, which are the main target of toxicogenomics databases. Here, we developed a deconvolution method for rats to retrieve information regarding immune cells from toxicogenomics databases. The rat-specific deconvolution showed high correlations for several types of immune cells between spleen and blood, and between liver treated with toxicants compared with those based on human and mouse data. Additionally, we found 4 clusters of compounds in Open TG-GATEs database based on estimated immune cell trafficking, which are different from those based on transcriptome data itself. The contributions of this work are three-fold. First, we obtained the gene expression profiles of 6 rat immune cells necessary for deconvolution. Second, we clarified the importance of species differences on deconvolution. Third, we retrieved immune cell trafficking from toxicogenomics databases. Accumulated and comparable immune cell profiles of massive data of immune cell trafficking in rats could deepen our understanding of enable us to clarify the relationship between the order and the contribution rate of immune cells, chemokines and cytokines, and pathologies. Ultimately, these findings will lead to the evaluation of organ responses in Adverse Outcome Pathway.

Choriocapillaris and progressive ganglion cell-inner plexiform layer loss in non-glaucomatous eyes

AIMS

To explore the relationship between choriocapillaris (CC) flow deficit percentage (FD%) and ganglion cell-inner plexiform layer (GCIPL) thickness in a population-based sample of non-glaucomatous eyes.

METHODS

This is a longitudinal cohort study and prospective cross-sectional study. Non-glaucoma Chinese subjects aged 18 years or older were enrolled. All participants underwent a detailed ophthalmic examination, including swept-source optical coherence tomography (SS-OCT) and SS-OCT angiography. Average, inner average, outer average and nine Early Treatment Diabetic Retinopathy Study sub-regions of GCIPL thickness and CC FD% were measured. The correlation between CC FD% and GCIPL was assessed using a linear regression model, and the relationship between the rate of change of GCIPL thickness and CC FD% was further validated in a 2year longitudinal study.

RESULTS

In the cross-sectional study including 3514 participants (3514 non-glaucoma eyes), a higher CC FD% was significantly associated with a thinner GCIPL (β=-0.32; 95% CI -0.43 to -0.21; p<0.001). Further, in a longitudinal study (453 eyes of 453 participants), a faster increase in CC FD% was found to be significantly associated with a faster decrease in GCIPL thickness (β=-0.10; 95% CI -0.17 to -0.03; p=0.004) after adjusting for age, sex, axial length and image quality score.

CONCLUSIONS

This is the first time to show that CC FD% and GCIPL thickness were correlated in both cross-sectional and longitudinal studies of non-glaucomatous individuals, which may potentially provide further insights on the role of CC perfusion in glaucoma development and progression.

Identification of differential immune cells and related diagnostic genes in patients with diabetic retinopathy

BACKGROUND

Diabetic retinopathy (DR) is a frequent microvascular abnormality associated with diabetes mellitus. The loss of retinal immunity is an important underlying mechanism of the DR pathogenesis, including the change in retinal immunosuppressive characteristics and the blood-retinal barrier disturbances. Therefore, this investigation screens immune-associated biomarkers in the retina of DR patients.

METHODS

In this investigation, the differential expression genes (DEGs) were acquired from Gene Expression Omnibus data GSE102485. The relative expression of 22 immune cell types in each sample was calculated by CIBERSORT analysis based on gene expression profile. The core module closely associated with immune infiltration was also screened by weighted gene co-expression network analysis (WGCNA). The overlapping DEGs and module genes were the differentially expressed immune-related genes (DEIRGs). With the help of the genes/proteins (STRING) database and MCODE plug-in, the protein-protein interaction (PPI) network hub genes were screened. Furthermore, the miRNA-hub genes and transcription factor (TF)-hub gene regulatory network were used to explain the possible signal pathways in DR. The hub genes verification was carried out by Polymerase Chain Reaction. Lastly, select CSF1R and its related pathway factor p-ERK1/2 to verify their expression in RF/6A under normal and high glucose environments.

RESULTS

A total of 3583 principle DEGs, that enriched immune-related GO terms and infection-related pathways were identified. CIBERSORT analysis showed that naive B cells, M2 macrophages, eosinophils, and neutrophil infiltration were significantly different. After intersecting 3583 DEGs, 168 DEIRGs and 181 module genes were identified. Furthermore, 15 hub genes, TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86, were identified via PPI network. The identified hub genes were up-regulated in DR and showed a high DR diagnostic value. Regulatory networks of the miRNA- and TF-hub genes can help understand the etiology of disease at the genetic level and optimize treatment strategy. CD14, VSIG4, HCK, and CSF1R were verified to be highly expressed in the vitreous of patients with DR. n RF/6A, CSF1R, and p-ERK1/2 were significantly overexpressed under high glucose conditions, with a statistically significant difference.

CONCLUSION

This investigation identified 15 genes (TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86) as hub DR genes, which may serve as a new potential point for the diagnosis and treatment of DR. CSF1R/p-ERK1/2 signaling may promotes the development of retinal neovascularization.

Choriocapillaris flow deficit and the risk of referable diabetic retinopathy: a longitudinal SS-OCTA study

AIMS

To investigate the association between the choriocapillaris flow deficit percentage (CC FD%) and the 1-year incidence of referable diabetic retinopathy (RDR) in participants with type 2 diabetes mellitus (DM).

METHODS

This prospective cohort study included participants with type 2 DM. The DR status was graded based on the ETDRS-7 photography. The CC FD% in the central 1 mm area, inner circle (1.5 mm to 2.5 mm), outer circle (2.5 mm to 5.0 mm) and the entire area in the macular region were measured using swept-source optical coherence tomography angiography (SS-OCTA). Logistic regression analysis was used to examine the association between baseline CC FD% and 1-year incident RDR.

RESULTS

A total of 1222 patients (1222 eyes, mean age: 65.1±7.4 years) with complete baseline and 1-year follow-up data were included. Each 1% increase in baseline CC FD% was significantly associated with a 1.69 times (relative risk 2.69; 95% CI 1.53 to 4.71; p=0.001) higher odds for development of RDR after 1-year follow-up, after adjusting for other confounding factors.

CONCLUSIONS

A greater baseline CC FD% detected by SS-OCTA reliably predicted higher risks of RDR in participants with type 2 DM. Thus, CC FD% may act as a novel biomarker for predicting the onset and progression of DR.

Cross-species scRNA-seq reveals the cellular landscape of retina and early alterations in type 2 diabetes mice

Single-cell RNA sequencing (scRNA-seq) analysis have provided an unprecedented resolution for the studies on diabetic retinopathy (DR). However, the early changes in the retina in diabetes remain unclear. A total of 8 human and mouse scRNA-seq datasets, containing 276,402 cells were analyzed individually to comprehensively delineate the retinal cell atlas. The neural retinas were isolated from the type 2 diabetes (T2D) and control mice, and scRNA-seq analysis was conducted to evaluate the early effects of diabetes on the retina. Bipolar cell (BC) heterogeneity were identified. We found some stable BCs across multiple datasets, and explored their biological functions. A new RBC subtype (Car8_RBC) in the mouse retina was validated using the multi-color immunohistochemistry. AC149090.1 was significantly upregulated in the rod cells, ON cone BCs (CBCs), OFF CBCs, and RBCs in T2D mice. Additionally, the interneurons, especially BCs, were the most vulnerable cells to diabetes by integrating scRNA-seq and genome-wide association studies (GWAS) analyses. In conclusion, this study delineated a cross-species retinal cell atlas and uncovered the early pathological alterations in the retina of T2D mice.

TAK1 blockade as a therapy for retinal neovascularization

Retinal neovascularization, or pathological angiogenesis in the retina, is a leading cause of blindness in developed countries. Transforming growth factor-β-activated kinase 1 (TAK1) is a mitogen-activated protein kinase kinase kinase (MAPKKK) activated by TGF-β1 and other proinflammatory cytokines. TAK1 is also a key mediator of proinflammatory signals and plays an important role in maintaining vascular integrity upon proinflammatory cytokine stimulation such as TNFα. However, its role in pathological angiogenesis, particularly in retinal neovascularization, remains unclear. Here, we investigate the regulatory role of TAK1 in human endothelial cells responding to inflammatory stimuli and in a rat model of oxygen-induced retinopathy (OIR) featured retinal neovascularization. Using TAK1 knockout human endothelial cells that subjected to inflammatory stimuli, transcriptome analysis revealed that TAK1 is required for activation of NFκB signaling and mediates its downstream gene expression related to endothelial activation and angiogenesis. Moreover, pharmacological inhibition of TAK1 by 5Z-7-oxozeaenol attenuated angiogenic activities of endothelial cells. Transcriptome analysis also revealed enrichment of TAK1-mediated NFκB signaling pathway in the retina of OIR rats and retinal neovascular membrane from patients with proliferative diabetic retinopathy. Intravitreal injection of 5Z-7-oxozeaenol significantly reduced hypoxia-induced inflammation and microglial activation, thus attenuating aberrant retinal angiogenesis in OIR rats. Our data suggest that inhibition of TAK1 may have therapeutic potential for the treatment of retinal neovascular pathologies.

Bioinformatics Tools for Bulk Gene Expression Deconvolution in Diabetic Retinopathy

Retinal neovascularization is one of the leading causes of vision loss and a hallmark of proliferative diabetic retinopathy (PDR). The immune system is observed to be involved in the pathogenesis of diabetic retinopathy (DR). The specific immune cell type that contributes to retinal neovascularization can be identified via a bioinformatics analysis of RNA sequencing (RNA-seq) data, known as deconvolution analysis. Previous study has identified the infiltration of macrophages in the retina of rats with hypoxia-induced retinal neovascularization and patients with PDR through a deconvolution algorithm, known as CIBERSORTx. Here, we describe the protocols of using CIBERSORTx to perform the deconvolution analysis and downstream analysis of RNA-seq data.

Oct4 cooperates with c-Myc to improve mesenchymal-to-endothelial transition and myocardial repair of cardiac-resident mesenchymal stem cells

BACKGROUND

Cardiac-resident mesenchymal stem cells (cMSCs) can exhibit fibrotic, proinflammatory, and proangiogenic phenotype in response to myocardial ischemia (Isch). How their phenotypic fate decisions are determined remains poorly understood. Here, we demonstrate that the cooperation of Oct4 and c-Myc in cMSCs creates a preferable mesenchymal-to-endothelial transition (MEndoT) to promote angiogenesis and consequent myocardial repair.

METHODS

We collected MSCs from cardiac and peripheral blood of rat with left ventricular Isch (LV Isch) 30 days after myocardial infarction (MI) or sham operation. After a comparison of characterization between cMSCs and peripheral blood MSCs (pbMSCs), we conducted transcriptome analysis and RNA sequencing of cMSCs. Using loss/gain-of-function approaches to understand the cooperation of c-Myc and Oct4 on MEndoT of cMSCs under hypoxic condition, we explored the mechanisms through transcriptome and functional experiment, and chromatin immunoprecipitation. Next, we transplanted male cMSCs with overexpression or inhibition of c-Myc/Oct4 into the infarcted myocardium of female rats and evaluated infarct size, cell retention, inflammation, remodeling, and function after 30 days.

RESULTS

LV Isch switched cMSCs toward both inflammatory and proangiogenic phenotypes, with increased secretion of inflammatory cytokines as well as decreased expression of proangiogenic factors. The effect of LV Isch on pbMSCs was less remarkable. Gene expression heatmap showed imbalance in expression of Oct4 and c-Myc regulating genes associated with remodeling of cMSCs. We provided evidence that cMSCs-specific c-Myc- versus Oct4-overexpression showed divergent genomic signatures, and their corresponding target genes play an important role in regulating cMSCs phenotypic changes. In particular, Oct4 accelerated angiogenesis induced by c-Myc overexpression in cMSCs and inhibited their phenotypic transition into inflammatory cells and fibroblast. Mechanistically, exogenous Oct4 caused c-Myc to translocate from the nucleus to the cytoplasm and activated some of its target signalings including VEGF signaling. Although transplantation of cMSCs alone did not improve LV remodeling and function, cMSCs co-transfected with c-Myc and Oct4 promoted a more positive effect in their survival and reparative properties, increased animal survival, reduced infarct size, decreased scar thickness, inhibited LV remodeling, and improved heart function 30 days after MI. Significantly, Oct4 promoted MEndoT ("Rescue me" signal) of cMSCs after both c-Myc stimulation in vitro and transplantation into the infarcted heart.

CONCLUSIONS

Myocardial Isch drives resident cMSCs toward multiple phenotypes. Oct4 interacts with c-Myc to promote MEndoT capacity of cMSCs and improve their survival and reparative effects through upregulation of angiogenesis-related signaling pathways. These findings may identify novel targets for stem cell therapy.

Macrophages in close proximity to the vitreoretinal interface are potential biomarkers of inflammation during retinal vascular disease

Background

Diabetic retinopathy and retinal vein occlusion are vision threatening retinal vascular diseases. Current first-line therapy targets the vascular component, but many patients are treatment-resistant due to unchecked inflammation. Non-invasive inflammatory imaging biomarkers are a significant unmet clinical need for patients. Imaging of macrophage-like cells on the surface of the retina using clinical optical coherence tomography (OCT) is an emerging field. These cells are increased in patients with retinal vascular disease, and could be a potential inflammatory biomarker. However, since OCT is limited by an axial resolution of 5–10 microns, the exact location and identity of these retinal cells is currently unknown.

Methods

We performed OCT followed by confocal immunofluorescence in wild-type mice to identify macrophages within 5–10 microns of the vitreoretinal interface. Next, we used Cx3cr1^CreER/+; Rosa26^zsGreen/+ mice to fate map retinal surface macrophages. Using confocal immunofluorescence of retinal sections and flatmounts, we quantified IBA1⁺Tmem119⁺CD169^neg microglia, IBA1⁺Tmem119^negCD169^neg perivascular macrophages, and IBA1⁺Tmem119^negCD169⁺ vitreal hyalocytes. Finally, we modeled neuroinflammation with CCL2 treatment and characterized retinal surface macrophages using flow cytometry, OCT, and confocal immunofluorescence.

Results

We were able to detect IBA1⁺ macrophages within 5–10 microns of the vitreoretinal interface in wild-type mice using OCT followed by confirmatory confocal immunofluorescence. Retinal surface macrophages were 83.5% GFP⁺ at Week 1 and 82.4% GFP⁺ at Week 4 using fate mapping mice. At steady state, these macrophages included 82% IBA1⁺Tmem119⁺CD169^neg microglia, 9% IBA1⁺Tmem119^negCD169⁺ vitreal hyalocytes, and 9% IBA1⁺Tmem119^negCD169^neg perivascular macrophages. After CCL2-driven neuroinflammation, many Ly6C⁺ cells were detectable on the retinal surface using OCT followed by confocal immunofluorescence.

Conclusions

Macrophages within close proximity to the vitreoretinal interface are self-renewing cells, and predominantly microglia with minor populations of perivascular macrophages and vitreal hyalocytes at steady state. In the context of neuroinflammation, monocytes and monocyte-derived macrophages are a significant component of retinal surface macrophages. Human OCT-based imaging of retinal surface macrophages is a potential biomarker for inflammation during retinal vascular disease.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12974-022-02562-3.

Retinal Transcriptome and Cellular Landscape in Relation to the Progression of Diabetic Retinopathy

Purpose

Previous studies that identify putative genes associated with diabetic retinopathy are only focusing on specific clinical stages, thus resulting genes are not necessarily reflective of disease progression. This study identified genes associated with the severity level of diabetic retinopathy using the likelihood-ratio test (LRT) and ordinal logistic regression (OLR) model, as well as to profile immune and retinal cell landscape in progressive diabetic retinopathy using a machine learning deconvolution approach.

Methods

This study used a published transcriptomic dataset (GSE160306) from macular regions of donors with different degrees of diabetic retinopathy (10 healthy controls, 10 cases of diabetes, 9 cases of nonproliferative diabetic retinopathy, and 10 cases of proliferative diabetic retinopathy or combined with diabetic macular edema). LRT and OLR models were applied to identify severity-associated genes. In addition, CIBERSORTx was used to estimate proportional changes of immune and retinal cells in progressive diabetic retinopathy.

Results

By controlling for gender and age using LRT and OLR, 50 genes were identified to be significantly increased in expression with the severity of diabetic retinopathy. Functional enrichment analyses suggested these severity-associated genes are related to inflammation and immune responses. CCND1 and FCGR2B are further identified as key regulators to interact with many other severity-associated genes and are crucial to inflammation. Deconvolution analyses demonstrated that the proportions of memory B cells, M2 macrophages, and Müller glia were significantly increased with the progression of diabetic retinopathy.

Conclusions

These findings demonstrate that deep analyses of transcriptomic data can advance our understanding of progressive ocular diseases, such as diabetic retinopathy, by applying LRT and OLR models as well as bulk gene expression deconvolution.

Exploring the Immune Infiltration Landscape and M2 Macrophage-Related Biomarkers of Proliferative Diabetic Retinopathy

BACKGROUNDS

Diabetic retinopathy (DR), especially proliferative diabetic retinopathy (PDR), is the major cause of irreversible blindness in the working-age population. Increasing evidence indicates that immune cells and the inflammatory microenvironment play an important role during PDR development. Herein, we aim to explore the immune landscape of PDR and then identify potential biomarkers correlated with specific infiltrating immune cells.

METHODS

We mined and re-analyzed PDR-related datasets from the Gene Expression Omnibus (GEO) database. Using the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm, we investigated the infiltration of 22 types of immune cells in all selected samples; analyses of differences and correlations between infiltrating cells were used to reveal the immune landscape of PDR. Thereafter, weighted gene co-expression network analysis (WGCNA) and differential expression analysis were applied to identify the hub genes on M2 macrophages that may affect PDR progression.

RESULTS

Significant differences were found between infiltration levels of immune cells in fibrovascular membranes (FVMs) from PDR and normal retinas. The percentages of follicular helper T cells, M1 macrophages, and M2 macrophages were increased significantly in FVMs. Integrative analysis combining the differential expression and co-expression revealed the M2 macrophage-related hub genes in PDR. Among these, COL5A2, CALD1, COL6A3, CORO1C, and CALU showed increased expression in FVM and may be potential biomarkers for PDR.

CONCLUSIONS

Our findings provide novel insights into the immune mechanisms involved in PDR. COL5A2, CALD1, COL6A3, CORO1C, and CALU are M2 macrophage-related biomarkers, further study of these genes could inform novel ideas and basis for the understanding of disease progression and targeted treatment of PDR.