Skip to Main Content

Dmitry V. Ivanov, Ph.D.

Dmitry V. Ivanov, Ph.D.

 

Research Subject

Signaling cascades and the epigenetic mechanisms involved in ocular development, degeneration, and regeneration. 

Focus

Retinal Neurogenesis, Ischemia and Optic Neuropathies, Regenerative Ophthalmology 

Published Articles


Contact

Office: 305-482-4230
Laboratory: 305-482-4796
DIvanov@med.miami.edu

Roles

Research Associate Professor of Ophthalmology
 

Summary

Significant progress has been made in regenerative ophthalmology, thanks to an understanding of the molecular mechanisms regulating ocular development. However, much remains to be discovered to improve regeneration of damaged or lost ocular tissues in order to restore vision in people who have lost their sight. The ongoing studies in Dr. Ivanov’s laboratory are aimed at exploring the signaling cascades and the epigenetic mechanisms involved in ocular development and regeneration, with a specific focus on neurogenesis in the developing retina and on strategies geared towards stimulating neuronal regeneration in the adult retina. The second important direction of Dr. Ivanov’s laboratory research has been to understand the role and mechanism of sterile inflammation, or innate immune response in the absence of live pathogens, in the pathophysiology of retinal disorders, with a specific interest in the contribution of a signal for “danger” (the so called damage-associated molecular patterns or DAMPs) and pattern recognition receptors.

Current Research

1. The role of the DNA demethylation pathway in retinal development: Understanding the mechanisms of retinal development is of vital importance in the proposal of therapeutic approaches to restoring visual function via the regeneration of lost retinal neurons. Though much progress has been made in the understanding of signaling cascades driving retinal development, the role of epigenetic mechanisms remains to be explored as meticulously. In order to fill this gap, we evaluated the contribution of the DNA methylation and DNA demethylation pathways to retinal development in recent studies. To this end, we studied DNA methylation in genomes of retinal progenitor cells (RPCs) and retinal neurons using a combination of whole genome bisulfite sequencing (WGBS) data and bioinformatic approaches (Figure 1). Our data suggest that the DNA demethylation pathway—not the DNA methylation pathway—is crucial for retinal development.

  1. Dvoriantchikova, G., Seemungal, R.J., & Ivanov, D. (2019) The epigenetic basis for the impaired ability of adult murine retinal pigment epithelium cells to regenerate retinal tissue. Sci Rep. Mar 7;9(1):3860. doi: 10.1038/s41598-019-40262-w. PubMed PMID: 30846751; PubMed Central PMCID: PMC6405859.
  2. Dvoriantchikova, G., Seemungal, R.J., & Ivanov, D. (2019). Development and epigenetic plasticity of murine Müller glia. Biochim Biophys Acta Mol Cell Res. Oct;1866(10):1584-1594. doi: 10.1016/j.bbamcr.2019.06.019. Epub 2019 Jul 2. PubMed PMID: 31276697.
  3. Dvoriantchikova, G., Seemungal, R.J., & Ivanov, D. (2019). DNA Methylation Dynamics During the Differentiation of Retinal Progenitor Cells Into Retinal Neurons Reveal a Role for the DNA Demethylation Pathway. Front. Mol. Neurosci. 12:182. doi: 10.3389/fnmol.2019.00182
Figure 1 
Figure 1. The analysis of DNA methylation in promoters of a subpopulation of photoreceptor and phototransduction genes revealed different dynamics of cytosine methylation in different cell types at different stages of embryogenesis. A) Mean methylation levels were calculated using the “methylKit” and “MethylSeekR” software packages (RPCs- retinal progenitor cells; RGCs-retinal ganglion cells; HC-horizontal cells; SBAC- starburst amacrine cells). B) Mean DNA methylation levels based on the methylation of individual CpGs in the promoter and first exon regions of photoreceptor and phototransduction genes were reduced in mature photoreceptors during retinal development. C) Reduced methylation of cytosines in close proximity to a transcription start site (TSS) in photoreceptor genes was accompanied by increased expression of these genes. (Gene_Normalized-CPM is the normalized gene level at counts-per-million)

 

2. Notch signaling in ocular development: The Dll1/Jag1/Notch pathway is a highly sophisticated signaling cascade, controlling cell-fate and tissue patterning with major cellular processes depending on the levels of Notch ligands, Dll1, and Jag1 (Figure 2). Dll1/Notch signaling, via a lateral inhibition mechanism, promotes a “salt-and-pepper” pattern when neighboring cells adopt two different fates (sender “S” and receiver “R”). Jag1/Notch, via lateral induction, drives neighboring cells to adopt the same fate—a hybrid “S/R” phenotype. The Jag1/Notch phenotype involves a double positive feedback loop, giving it an advantage over the Dll1/Notch phenotype: the Jag1/Notch phenotype promotes itself. Meanwhile, fringe proteins (Lfng and Mfng) switch Notch signaling from lateral induction to lateral inhibition, thereby promoting Dll1/Notch signaling over Jag1/Notch. Our data and literature suggest that retinal progenitor cells (RPCs) at the early stage of retinal development, and developing Müller glia at the late stage of retinal development, adopt the “R” Dll1/Notch-regulated fate, while RPCs differentiating into retinal neurons adopt the “S” phenotype. At the same time, our data and literature suggest that lacrimal gland epithelial cells have the typical Jag1/Notch hybrid “S/R” phenotype and easily undergo an epithelial-to-mesenchymal transition (EMT). We also found that Notch signaling regulates branching morphogenesis in the developing lacrimal gland. Our data and literature suggest that RPE cells also have the typical Jag1/Notch hybrid “S/R” phenotype. Thus, Notch signaling plays critical roles in many aspects of ocular organogenesis and by learning how to satisfactorily manipulate Notch signaling, we may significantly improve latent regenerative abilities inherent in ocular tissues.

  1. Dvoriantchikova, G., Perea-Martinez, I., Pappas, S., Barry, A.F., Danek, D., Dvoriantchikova, X., Pelaez, D., & Ivanov, D. (2015). Molecular Characterization of Notch1 Positive Progenitor Cells in the Developing Retina. PLoS One.10(6), e0131054. PMCID: PMC4474692.
  2. Dvoriantchikova, G., Tao, W., Pappas, S., Gaidosh, G., Tse, D.T., Ivanov, D*., & Pelaez, D*. (2017). Molecular Profiling of the Developing Lacrimal Gland Reveals Putative Role of Notch Signaling in Branching Morphogenesis. Invest Ophthalmol Vis Sci. 58(2), 1098-1109. PMCID: PMC5308770. * - DI and DP are joint senior authors
  3. Dvoriantchikova, G., Seemungal, R.J., & Ivanov, D. (2019). Development and epigenetic plasticity of murine Müller glia. Biochim Biophys Acta Mol Cell Res. Oct;1866(10):1584-1594. doi: 10.1016/j.bbamcr.2019.06.019. Epub 2019 Jul 2. PubMed PMID: 31276697.
  4. Ivanov, D. (2019), Notch signaling-induced oscillatory gene expression may drive neurogenesis in the developing retina. Front. Mol. Neurosci. Sep 19;12:226. doi: 10.3389/fnmol.2019.00226. eCollection 2019. PMID: 31607861 PMCID: PMC6761228

Figure 2

Figure 2. Notch-Delta-Jagged signaling: A) The Notch pathway is activated when the Notch receptor of one cell interacts with the ligand of a neighboring cell leading to cleavage of the Notch intracellular domain (NICD) and its release into the cytoplasm. NICD acts as a transcription factor and controls the expression of many genes, including Notch receptors and ligands. However, while it directly activates the expression of Notch receptors, the Jag1 ligand, and transcription factor Hes1 (which acts as an inhibitor of any gene expression), it indirectly inhibits Dll1 expression through Hes1. The special family of fringe proteins (Lfng and Mfng) increases the Notch receptor’s affinity to bind to Dll1 and decreases it for Jag1, thus promoting lateral inhibition over lateral induction. B) Jag1/Notch signaling forms a double positive feedback loop between the two neighboring cells and forces them to adopt the same fate/phenotype: high expressions of the Notch receptor, Jag1, Hes1, and low Dll1 expression. The Jag1/Notch cells both send (due to Jag1 ligands) and receive (due to Notch receptors) signals (a so-called hybrid Sender/Receiver (S/R) phenotype). The mechanism that promotes this phenotype is known as lateral induction. C) Dll1/Notch signaling causes a double negative feedback loop between the two neighboring cells promoting them to acquire two opposite fates/phenotypes (a “salt-and pepper” pattern): Sender (S) (high Dll1; low Notch, Hes1, and Jag1) and Receiver (R) (high Notch and Hes1; low Dll1 and Jag1). The mechanism that promotes the two opposite fates/phenotypes is known as lateral inhibition.

 

3. Cell death and inflammation: Common forms of vision loss occur when retinal ganglion cells (RGCs) undergo apoptosis and/or necrosis in the retina. Apoptosis, however, is not as dangerous to the surrounding tissue as necrosis. Apoptotic cell death stimulates the production of anti-inflammatory and neuroprotective factors from immune cells that have internalized the apoptotic cells. Our studies indicate that therapeutic strategies based on mimicking a systemic increase in levels of apoptotic signals can significantly reduce retinal injury. In contrast, endogenous factors called damage-associated molecular patterns (DAMPs) liberated from necrotic cells mediate cytotoxic, pro-inflammatory responses in retinal tissue. We demonstrated that these DAMPs, released from lysed necrotic cells, lead to inflammation and retinal damage. We also found that suppressing neuronal necrosis in the retina promotes a neuroprotective environment and reduces tissue damage. Thus, in contrast to apoptosis, necrosis can trigger further RGC death and retinal damage. Historically viewed as an entirely accidental and unregulated cellular event, we now know that that necrosis, like apoptosis, can be regulated and executed by programmed mechanisms (“necroptosis”). We demonstrated that necroptosis contributes to retinal injury through direct loss of RGCs and induction of associated inflammatory responses. Since necroptosis can be regulated, research into its exact mechanisms harbors colossal translational value that could lead to novel therapies. The effectiveness of some of these therapies has already been demonstrated in our published studies.

  1. Dvoriantchikova, G., Agudelo, C., Hernandez, E., Shestopalov, V.I., & Ivanov, D. (2009). Phosphatidylserine-containing liposomes promote maximal survival of retinal neurons after ischemic injury. J Cereb Blood Flow Metab., 29(11), 1755-1759. 
  2. Dvoriantchikova, G., Degterev, A., & Ivanov, D. (2014). Retinal ganglion cell (RGC) programmed necrosis contributes to ischemia-reperfusion-induced retinal damage. Exp Eye Res. 123:1-7. PMCID: PMC4059599.
  3. Santos, A.R., Dvoriantchikova, G., Li, Y., Mohammad, G., Abu El-Asrar, A.M., Wen, R., & Ivanov, D. (2014). Cellular mechanisms of high mobility group 1 (HMGB-1) protein action in the diabetic retinopathy. PLoS One., 9(1), e87574. PMCID: PMC3909191
  4. Madsen, P.M., Pinto, M., Patel, S., McCarthy, S., Gao, H., Taherian, M., Karmally, S., Pereira, C.V., Dvoriantchikova, G., Ivanov, D., Tanaka, K.F., Moraes, C.T., & Brambilla, R. (2017). Mitochondrial DNA Double-Strand Breaks in Oligodendrocytes Cause Demyelination, Axonal Injury, and CNS Inflammation. J Neurosci. 37(42), 10185-10199. PMCID: PMC5647772.
 

4. Molecular mechanisms of sterile inflammation in the retina: It is known that sterile inflammation, or the innate immune response in the absence of live pathogens, is a key player in the pathogenesis of many ocular diseases. But what are the sources of sterile inflammation? Identifying and eliminating such sources/triggers could ease degenerative conditions by addressing their root causes—rather than simply covering up symptoms. My lab’s research brings us closer to providing an answer to this and related questions. We demonstrated that after engaging DAMPs (Hsp70, Hmgb1, etc.), pattern recognition receptors (PRRs), such as Tlr4 and Rage, activate signaling cascades that trigger inflammation and retinal damage. We also identified new PRR-dependent signaling cascades that mediate retinal damage. We found that the Tlr4/Trif-dependent signaling cascade contributes to retinal damage both directly (through loss of RGCs) and indirectly (through induction of neurotoxic pro-inflammatory responses). The results of our work provide an intellectual foundation for the development of new therapeutic strategies that could reduce neurotoxic, pro-inflammatory responses specifically in the retina without globally suppressing the immune system (Figure 3).

  1. Dvoriantchikova, G., Hernandez, E., Grant, J., Santos, A.R., Yang, H., & Ivanov, D. (2011). The high-mobility group box-1 nuclear factor mediates retinal injury after ischemia reperfusion. Invest Ophthalmol Vis Sci., 52(10), 7187-7194. PMCID: PMC3207720
  2. Dvoriantchikova, G., Santos, A.R., Saeed, A.M., Dvoriantchikova, X., & Ivanov, D. (2014). Putative role of protein kinase C in neurotoxic inflammation mediated by extracellular heat shock protein 70 after ischemia-reperfusion. J Neuroinflammation., 11, 81. PMCID: PMC4001362
  3. Dvoriantchikova, G., Santos, A.R., Danek, D., Dvoriantchikova, X., & Ivanov, D. (2014). The TIR-domain-containing adapter inducing interferon-β-dependent signaling cascade plays a crucial role in ischemia-reperfusion-induced retinal injury, whereas the contribution of the myeloid differentiation primary response 88-dependent signaling cascade is not as pivotal. Eur J Neurosci., 40(3), 2502-2512. PMCID: PMC4122625
  4. Tse, B.C., Dvoriantchikova, G., Tao, W., Gallo, R.A., Lee, J.Y., Pappas, S., Brambilla, R., Ivanov, D., Tse, D.T. & Pelaez, D. (2018). Tumor Necrosis Factor Inhibition in the Acute Management of Traumatic Optic Neuropathy. Invest Ophthalmol Vis Sci. 59(7), 2905-2912. PMCID: PMC5989875.

Figure 3

Figure 3. The “damage chain reaction”