About our lab
We are a multidisciplinary group united by a passion for vision restoration. We develop novel therapies for glaucoma, traumatic optic neuropathies, optic pathway glioma, and other diseases characterized by retinal ganglion cell and photoreceptor loss. To achieve this audacious goal, we combine the achievements in regenerative medicine, retinal cell biology and development, advanced transcriptomics, transplantation, and functional imaging of the retinal neurons on a single cell level.
We employ automation, artificial intelligence, and quantitative strategies to produce retinal and other organoids from human, tree shrew, and mouse stem cells. We are particularly interested in using this fascinating model to test therapies, study cell-cell interaction, model diseases, such as Alzheimer's, LHON, NAION, and glaucoma.
We perform deep advanced analysis of single-cell RNA-, ATAC-, ChIP-, VDJ-, and spatial-seq data, focusing on cell specification, maturation, and cell-to-cell communication in disease and regeneration. Species include humans, dogs, mice, and axolotl. The ultimate goal is to create a “digital eye” - in silico platform to model, explore and predict cell behavior in changing ecosystem.
Organoids: retina and beyond
Integrated multi-omics analysis
Competences
Transplantation and cell therapy development
The retina of the eye provides a unique setting to study and control donor cell fate on a single level. The lab focuses on cell and organoid transplantation, emphasizing the microenvironment and its role in donor cell maturation and integration.
Team
Petr Baranov
Head of the Lab
My lab is committed to search for novel therapies for glaucoma, traumatic optic neuropathies and other diseases characterized by retinal ganglion cell loss. We explore cell replacement and neuroprotection strategies. To achieve this audacious goal we combine the achievements in regenerative medicine, retinal cell biology and development, transplantation and functional imaging of the retinal neurons on single cell level.
Yasaman Anvarinia
Joint Postdoctoral fellow, MD (Rizzo Lab)
Coming from a clinical background and with a lifelong passion for research, I’m excited to contribute to advancements in visual neurosciences, particularly in understanding and addressing optic neuropathies like non-arteritic anterior ischemic optic neuropathy (NAION). To me, research is where you get to glimpse—and maybe even create—the future of medicine! I like to bridge the gap between translational research and clinical practice, bringing innovative discoveries closer to improving patient care.
Nikita Bagaev
Postdoctoral fellow, MD
I am focused on Neurofibromatosis Type 1 (NF1) studies. In children suffering from this genetic condition multiple neural tissue derived tumors arise. They that develop along the optic pathway result in early vision loss in these patients. Due to scarcity of these clinical cases we use mouse models of NF1 to explore biology of these rare tumors. Combining experimental data obtained from mice and single-cell transcriptomics data we hope to untangle mechanisms of disease progression and find a cure potentially.
Ekaterina Ivleva
Scientific Associate
Having experience with bulk RNA-seq data, I joined the lab to work on single-cell transcriptomics. I believe that collecting high-quality data followed by accurate single-cell analysis can provide significant biological insights in the field of ophthalmology. My primary goal is to create a single-cell atlas of the cornea for both healthy and keratoconus patients, aiming to define the involvement of each cell type during disease progression, cell–cell communication, and other molecular mechanisms underlying keratoconus development.
Emil Kriukov
Lead Bioinformatician
My primary goal of the research is to build the biggest picture possible of cell ontogeny in dynamics using multiomics data and computational approaches. By the ontogeny, cell-fate-wise, I understand all the changes occurring, including development, aging, disease, and, of course, the route retinal ganglion cells have to undergo from differentiation to their functional integration upon transplantation.
Everett Labrecque
Student Intern
This is my first time being so close to medical research! It has been a dream of mine since I was a small boy. As a slightly larger boy, it is a thrill to help with real medical work. I am excited to be analyzing data, and I'm looking forward to working with the people in Baranov’s lab!
Volha Malechka
Postdoctoral fellow, MD
My long-term career goal is to contribute to ophthalmology field in improving and restoring human vision by constantly building up strong scientific knowledge and clinical skills.
Nasrin Refaian
Postdoctoral fellow, PhD
Having experience in Ophthalmic Oncology, I joined the lab and learned stem cell culture techniques. My research interest lies within stem cell and retinal organoid models to improve retinal ganglion cell transplantation and their connectivity to the brain. I am very excited to be involved in the development of novel cell replacement therapies to treat retinal neurodegenerative diseases.
Jessica Sánchez
Student Intern
As a biomedical engineer pursuing a Master's in Tissue Engineering and Regenerative Medicine, I'm focused on developing regenerative strategies for retinal neurodegenerative diseases. My research aims to enhance retinal ganglion cell (RGC) maturation using neurotrophic factors through in vitro modeling. With experience in nanomaterials, biosensors, and image-based detection, I take a multidisciplinary approach to biomedical challenges.
Jonathan Soucy
Postdoctoral fellow, PhD
I am focused on improving the structural and functional integration of donor retinal ganglion cells by directing neural migration, controlling their microenvironment, and manipulating host neurons. I believe that we need a better understanding of fundamental principles that control donor neuron integration in the retina and brain to guide RGCs to their natural connecting points and improve cell replacement therapy outcomes. These include homophilic cell-cell interactions, chemokine signal cues, neurotrophic factors, migration modes, and neural activity.
Sthavir Vinjamuri
Student Intern
I am primarily focused on studying mice single-cell retinas of various genotypes. My goal is to streamline the accessibility of retinal data allowing for the efficient sharing and analysis of cell ontogeny. I strive to implement this ongoing experience to further improve patient outcomes in ophthalmology.
My research ...........
Outside of the lab, I am an avid runner, rock climber, ultimate frisbee player, and coffee enthusiast.
Alumni
Publications
Featured publications
The “in silico–in vitro–in vivo” funnel holds significant potential for identifying targets to control cellular processes in research and clinical applications. In this report, we describe a framework for identifying, selecting, and applying chemokines to direct retinal neuron migration in vivo within the adult mouse retina.
Controlling donor and newborn neuron migration and maturation in the eye through microenvironment engineering
Jonathan R. Soucy, Levi Todd, Emil Kriukov, Monichan Phay, Volha V. Malechka, John Dayron Rivera, Thomas A. Reh, Petr Baranov | PNAS | 2023
Johnson TV, Calkins DJ, Fortune B, Goldberg JL, La Torre A, Lamba DA, Meyer JS, Reh TA, Wallace VA, Zack DJ, Baranov P. | iScience | 2023
The importance of unambiguous cell origin determination in neuronal repopulation studies
Using the retina as an example, we discuss common reasons for artifactual labeling of endogenous host neurons with donor cell reporters and suggest strategies to prevent erroneous conclusions based on misidentification of cell origin.
Soucy JR et al. | Mol Neurodegeneration | 2023
Retinal ganglion cell repopulation for vision restoration in optic neuropathy: a roadmap from the RReSTORe Consortium
The RReSTORe Consortium outlines a comprehensive roadmap for retinal ganglion cell (RGC) repopulation to restore vision lost due to optic neuropathies. They identify five critical areas: RGC development and differentiation, transplantation methods and models, RGC survival and maturation, inner retinal wiring, and eye-to-brain connectivity. By addressing these challenges through multidisciplinary approaches, the consortium aims to advance therapeutic strategies for vision restoration.
J. Oswald, E. Kegeles, T. Minelli, P. Volchkov, P. Baranov | Mol Ther Methods Clin Dev. | 2021
Transplantation of miPSC/mESC-derived retinal ganglion cells into healthy and glaucomatous retinas
Optic neuropathies, including glaucoma, are a group of neurodegenerative diseases, characterized by the progressive loss of retinal ganglion cells (RGCs), leading to irreversible vision loss. While previous studies demonstrated the potential to replace RGCs with primary neurons from developing mouse retinas, their use is limited clinically.
E. Kegeles, A. Naumov, E. Karpulevich, P. Volchkov, P. Baranov | Front Neurosci. | 2020
Convolutional Neural Networks Can Predict Retinal Differentiation in Retinal Organoids
We have developed a deep learning-based computer algorithm to recognize and predict retinal differentiation in stem cell-derived organoids based on bright-field imaging. The three-dimensional "organoid" approach for the differentiation of pluripotent stem cells (PSC) into retinal and other neural tissues has become a major in vitro strategy to recapitulate development.
Using scRNAseq, we assembled a comprehensive atlas of human fetal retina development from week 8 to week 27, focusing on retinal ganglion cells (RGC). By applying pseudotime analysis, we mapped continuous RGC maturation trajectories, uncovering intrinsic and extrinsic profiles, including key maturation drivers. Our findings enhance understanding of retinal development, providing a valuable reference tool for automated annotation and developmental analyses.
Unraveling the developmental heterogeneity of human retinal ganglion cells within the developing retina to study to the continuity of maturation
Emil Kriukov, Jonathan R. Soucy, Everett Labrecque, Petr Baranov | Developmental Biology | 2025
J. Oswald, P. Baranov | Ther Adv Ophthalmol. | 2018
Regenerative medicine in the retina: from stem cells to cell replacement therapy
Following the fast pace of the growing field of stem cell research, retinal cell replacement is finally emerging as a feasible mean to be explored for clinical application. Although neuroprotective treatments are able to slow the progression of retinal degeneration caused by diseases such as age-related macular degeneration and glaucoma, they are insufficient to fully halt disease progression and unable to recover previously lost vision.
A slow-release cocktail of BDNF and GDNF markedly improves outcomes for stem-cell–derived retinal ganglion cell (RGC) therapy. In culture, the factors boosted RGC differentiation, survival, and spontaneous activity; in mouse optic-neuropathy models, co-treatment increased donor RGC survival ~2.7× (mouse→mouse) and ~15× (human→mouse) and also preserved host RGC function. The work shows that engineering the retinal microenvironment with sustained neurotrophic support can both protect vision and make RGC transplantation far more effective, offering a practical adjunct for glaucoma and other optic neuropathies across mild to severe disease stages.
Sustained Neurotrophic Factor Co-Treatment Enhances Donor and Host Retinal Ganglion Cell Survival in Mice
Jonathan R. Soucy; Julia Oswald; Emil Kriukov; Monichan Phay; John Masland; Christian Pernstich; Petr Baranov | TVST | 2025
We need your ideas and expertise to make Vision Restoration possible. Send your CV and short personal statement to Petr @ Mass Eye and Ear or in the form below if you believe that the Journey is the Reward.
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Partnership
The support from funding agencies allows us to develop novel cell-based therapies for blinding diseases, educate patients, families and invest in the next generation of brilliant scientists, ophthalmologists, physicians and entrepreneurs. We are grateful to The Gilbert Family Foundation, National Eye Institute, BrightFocus Foundation, Massachusetts Lions Club, The Iraty Award, Research to Prevent Blindness and private donors. Each contribution brings us a step closer to our Audacious Goal of Vision Restoration.
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We believe that the therapy development is a collaborative effort. We have extensive experience in partnering with pharmaceutical, biotech and academic labs around the world to move ideas from conception to clinical trial.
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