Neurovascular regulation in diabetic retinopathy and emerging therapies

Diabetic retinopathy (DR) is the leading cause of vision loss in working adults in developed countries. The disease traditionally classified as a microvascular complication of diabetes is now widely recognized as a neurovascular disorder resulting from disruption of the retinal neurovascular unit (NVU). The NVU comprising retinal neurons, glia and vascular cells coordinately regulates blood flow, vascular density and permeability to maintain homeostasis. Disturbance of the NVU during DR can lead to vision-threatening clinical manifestations. A limited number of signaling pathways have been identified for intercellular communication within the NVU, including vascular endothelial growth factor (VEGF), the master switch for angiogenesis. VEGF inhibitors are now widely used to treat DR, but their limited efficacy implies that other signaling molecules are involved in the pathogenesis of DR. By applying a novel screening technology called comparative ligandomics, we recently discovered secretogranin III (Scg3) as a unique DR-selective angiogenic and vascular leakage factor with therapeutic potential for DR. This review proposes neuron-derived Scg3 as the first diabetes-selective neurovascular regulator and discusses important features of Scg3 inhibition for next-generation disease-targeted anti-angiogenic therapies of DR.

Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy

Background

Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy.

Methods

We analyzed HLA-presented peptides by MS-based ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues, and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate targets with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from The Cancer Genome Atlas (TCGA KIRC, n = 452). DNA methylation (TCGA KIRC, n = 273), somatic mutations (TCGA KIRC, n = 392), and gene ontology (GO) and correlations with tumor metabolites (cohort 1, n = 30) and immune-oncological markers (cohort 1, n = 37) were analyzed to characterize regulatory and functional involvements. CD8⁺ T cell priming assays were used to identify immunogenic peptides. The candidate gene EGLN3 was functionally investigated in cell culture.

Results

A total of 34,226 HLA class I- and 19,325 class II-presented peptides were identified in ccRCC tissue, of which 443 class I and 203 class II peptides were ccRCC-specific and presented in ≥ 3 tumors. One hundred eighty-five of the 499 corresponding source genes were involved in pathways activated by ccRCC tumors. After validation in the independent cohort from TCGA, 113 final candidate genes remained. Candidates were involved in extracellular matrix organization, hypoxic signaling, immune processes, and others. Nine of the 12 peptides assessed by immunogenicity analysis were able to activate naïve CD8⁺ T cells, including peptides derived from EGLN3. Functional analysis of EGLN3 revealed possible tumor-promoting functions.

Conclusions

Integration of HLA ligandomics, transcriptomics, genetic, and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is recommended to expand the treatment landscape of ccRCC.

Comparative Ligandomic Analysis of Human Lung Epithelial Cells Exposed to PM 2.5

OBJECTIVE

To investigate whether exposure to particulate matter of diameter equal to or less than 2.5 μm (PM _2.5) alters the response of lung epithelial cells to extrinsic regulation by globally profiling cell surface ligands and quantifying their binding activity.

METHODS

Human A549 lung epithelial cells (LECs) were treated with or without PM _2.5. Ligandomic profiling was applied to these cells for the global identification of LEC-binding ligands with simultaneous quantification of binding activity. Quantitative comparisons of the entire ligandome profiles systematically identified ligands with increased or decreased binding to PM _2.5-treated LECs.

RESULTS

We found 143 ligands with increased binding to PM _2.5-treated LECs and 404 ligands with decreased binding. Many other ligands showed no change in binding activity. For example, apolipoprotein E (ApoE), Notch2, and growth arrest-specific 6 (Gas6) represent ligands with increased, decreased, or unchanged binding activity, respectively. Both ApoE and Gas6 are phagocytosis ligands, suggesting that phagocytic receptors on LECs after stimulation with PM _2.5 were differentially upregulated by PM _2.5.

CONCLUSION

These results suggest that the newly-developed ligandomics is a valuable approach to globally profile the response of LECs to PM _2.5 in terms of regulating the expression of cell surface receptors, as quantified by ligand binding activity. This quantitative ligandome profiling will provide in-depth understanding of the LEC molecular response on the cell surface to particulate matter air pollution.

Function-first ligandomics for ocular vascular research and drug target discovery

Human eyes may develop different vascular diseases with neovascularization and/or leakage, including wet age-related macular degeneration (AMD), diabetic macular edema (DME), proliferative diabetic retinopathy (PDR), retinopathy of prematurity, corneal neovascularization and intraocular tumors. A breakthrough in therapy is the advent and approval of vascular endothelial growth factor (VEGF) inhibitors. However, anti-VEGF drugs not only have limited efficacy to treat AMD, DME and PDR but also are not approved for other ocular indications. The key to addressing these unmet clinical needs is to develop novel therapies against VEGF-independent angiogenic factors or signaling pathways for alternative or combination therapy. We recently developed the first paradigm of ligandomics for global mapping of cell-wide ligands as well as disease-selective ligands. Therapies targeting disease-selective angiogenic or vascular leakage factors likely have high efficacy, minimal side effects, wide therapeutic windows and relatively low drug attrition rates. A critical challenge is how to distinguish between genuine drug targets and spurious hits identified by high-throughput ligandomics. Here we exploited the unique advantages of the eye and extracellular ligands by combining ligandomics with "function-first" and/or "therapy-first" analyses to efficiently characterize functional activity, disease selectivity, pathogenic role and therapeutic potential of identified ligands. The innovative function- or therapy-first ligandomics will systematically and reliably delineate disease-selective angiogenic or vascular leakage factors and markedly facilitate ocular vascular research and ligand-guided targeted anti-angiogenic therapy.

Secretogranin III: a diabetic retinopathy-selective angiogenic factor

Secretogranin III (Scg3) is a member of the granin protein family that regulates the biogenesis of secretory granules. Scg3 was recently discovered as an angiogenic factor, expanding its functional role to extrinsic regulation. Unlike many other known angiogenic factors, the pro-angiogenic actions of Scg3 are restricted to pathological conditions. Among thousands of quantified endothelial ligands, Scg3 has the highest binding activity ratio to diabetic vs. healthy mouse retinas and lowest background binding to normal vessels. In contrast, vascular endothelial growth factor binds to and stimulates angiogenesis of both diabetic and control vasculature. Consistent with its role in pathological angiogenesis, Scg3-neutralizing antibodies alleviate retinal vascular leakage in mouse models of diabetic retinopathy and retinal neovascularization in oxygen-induced retinopathy mice. This review summarizes our current knowledge of Scg3 as a regulatory protein of secretory granules, highlights its new role as a highly disease-selective angiogenic factor, and envisions Scg3 inhibitors as "selective angiogenesis blockers" for targeted therapy.