Ragini Ahanonu

All Publications

• Single-Cell Molecular Characterization of Uterine Carcinosarcoma Phansalkar, R., Wang, A., Al-Humadi, R., Nasr, S., Sandor, K., Lu, X., D'Ambrogia, K., Korgaonkar, K., Howitt, B. ELSEVIER SCIENCE INC. 2025

  View details for DOI 10.1016/j.labinv.2024.103291

  View details for Web of Science ID 001460372500042

• Single-cell transcriptomic analysis of corneal organoids during development. Stem cell reports Swarup, A., Phansalkar, R., Morri, M., Agarwal, A., Subramaniam, V., Li, B., Wu, A. Y. 2023

  Abstract

  Corneal organoids are useful tools for disease modeling and tissue transplantation; however, they have not yet been well studied during maturation. We characterized human iPSC-derived corneal organoids at 1, 2, 3, and 4 months of development using single-cell RNA sequencing to determine the cellular heterogeneity at each stage. We found pluripotent cell clusters committed to epithelial cell lineage at 1 month; early corneal epithelial, endothelial, and stromal cell markers at 2 months; keratocytes as the largest cell population at 3 months; and a large epithelial cell population at 4 months. We compared organoid to fetal corneal development at different stages and found that 4-month organoids closely resemble the corneal cellular complexity of the fetal (16 post conception week) and adult cornea. Using RNA velocity trajectory analysis, we found that less differentiated cells appear to give rise to corneal epithelial cells during development.

  View details for DOI 10.1016/j.stemcr.2023.10.022

  View details for PubMedID 38039970

• TDP43 pathology in chronic traumatic encephalopathy retinas. Acta neuropathologica communications Phansalkar, R., Goodwill, V. S., Nirschl, J. J., De Lillo, C., Choi, J., Spurlock, E., Coughlin, D. G., Pizzo, D., Sigurdson, C. J., Hiniker, A., Alvarez, V. E., Mckee, A. C., Lin, J. H. 2023; 11 (1): 152

  Abstract

  Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with repetitive head trauma. Brain pathology in CTE is characterized by neuronal loss, gliosis, and a distinctive pattern of neuronal accumulation of hyper-phosphorylated tau (p-tau) and phospho-TDP43 (p-TDP43). Visual anomalies have been reported by patients with CTE, but the ocular pathology underlying these symptoms is unknown. We evaluated retinal pathology in post-mortem eyes collected from 8 contact sport athletes with brain autopsy-confirmed stage IV CTE and compared their findings to retinas from 8 control patients without CTE and with no known history of head injury. Pupil-optic nerve cross sections were prepared and stained with hematoxylin and eosin (H&E), p-tau, p-TDP43, and total TDP43 by immunohistochemistry. No significant retinal degeneration was observed in CTE eyes compared to control eyes by H&E. Strong cytoplasmic p-TDP43 and total TDP43 staining was found in 6/8 CTE eyes in a subset of inner nuclear layer interneurons (INL) of the retina, while only 1/8 control eyes showed similar p-TDP43 pathology. The morphology and location of these inner nuclear layer interneurons were most compatible with retinal horizontal cells, although other retinal cell types present in INL could not be ruled out. No p-tau pathology was observed in CTE or control retinas. These findings identify novel retinal TDP43 pathology in CTE retinas and support further investigation into the role of p-TDP43 in producing visual deficits in patients with CTE.

  View details for DOI 10.1186/s40478-023-01650-6

  View details for PubMedID 37737191

  View details for PubMedCentralID 7914059

• Liver Pathology After Hematopoietic Stem Cell Transplantation. Surgical pathology clinics Phansalkar, R., Kambham, N., Charu, V. 2023; 16 (3): 519-532

  Abstract

  Hematopoietic stem cell transplantation is used to treat a variety of hematologic malignancies and autoimmune conditions. The immunosuppressive medications as well as other therapies used both before and after transplantation leave patients susceptible to a wide spectrum of complications, including liver injury. Causes for liver damage associated with stem cell transplantation include sinusoidal obstruction syndrome, graft-versus-host disease, iron overload, and opportunistic infection. Here, the authors review the clinical and pathological findings of these etiologies of liver injury and provide a framework for diagnosis.

  View details for DOI 10.1016/j.path.2023.04.007

  View details for PubMedID 37536886

• Chiasmal Injury in Silent Pituitary Apoplexy Without Evidence of Mass Effect. Journal of neuro-ophthalmology : the official journal of the North American Neuro-Ophthalmology Society Phansalkar, R., Navarro, S. E., Chiang, H., Moss, H. E. 2023

  View details for DOI 10.1097/WNO.0000000000001956

  View details for PubMedID 37459375

• Preparing the Ocular Surface for a Boston Keratoprosthesis Type 1 Through En Bloc Minor Salivary Gland Transplantation and Mucous Membrane Grafting in End-Stage Stevens-Johnson Syndrome. Cornea Arboleda, A., Phansalkar, R., Amescua, G., Lee, W. S., Brandt, J. D., Mannis, M. J., Kossler, A. L., Lin, C. C. 2023

  Abstract

  This case describes the successful visual restoration of a patient with end-stage Stevens-Johnson syndrome (SJS) with a severely keratinized ocular surface.This study is a case report.A 67-year-old man with SJS secondary to allopurinol sought visual rehabilitation options. His ocular surface was severely compromised from sequelae of chronic SJS, leaving him with light perception vision bilaterally. The left eye was completely keratinized with severe ankyloblepharon. The right eye had failed penetrating keratoplasty, limbal stem cell deficiency, and a keratinized ocular surface. The patient declined both a Boston type 2 keratoprosthesis and a modified osteo-odonto keratoprosthesis. Therefore, a staged approach was pursued with (1) systemic methotrexate to control ocular surface inflammation, (2) minor salivary gland transplant to increase ocular surface lubrication, (3) lid margin mucous membrane graft to reduce keratinization, and finally, (4) Boston type 1 keratoprosthesis for visual restoration. After minor salivary gland transplant and mucous membrane graft, the Schirmer score improved from 0 mm to 3 mm with improvement in ocular surface keratinization. This approach successfully restored the vision to 20/60, and the patient has retained the keratoprosthesis for over 2 years.Sight restoration options are limited in patients with end-stage SJS with a keratinized ocular surface, aqueous and mucin deficiency, corneal opacification, and limbal stem cell deficiency. This case demonstrates successful ocular surface rehabilitation and vision restoration in such a patient through a multifaceted approach that resulted in successful implantation and retention of a Boston type 1 keratoprosthesis.

  View details for DOI 10.1097/ICO.0000000000003262

  View details for PubMedID 37159138

• Reduction of Teprotumumab-Induced Hearing Loss With Comparable Efficacy Using Half-Dose Therapy. Ophthalmic plastic and reconstructive surgery Phansalkar, R., Lu, T., Alyono, J., Lee, J., Dosiou, C., Kossler, A. L. 2023

  Abstract

  Teprotumumab has been shown to be effective in the treatment of thyroid eye disease, a potentially vision-threatening condition. Adverse events, including sensorineural hearing loss, have been associated with teprotumumab. The authors present the case of a 64-year-old female who discontinued teprotumumab due to significant sensorineural hearing loss after 4 infusions, along with other adverse events. The patient was unresponsive to a subsequent course of intravenous methylprednisolone and orbital radiation, during which she experienced worsening thyroid eye disease symptoms. Teprotumumab was restarted 1 year later, at a half dose of 10mg/kg for 8 infusions. Three months post-treatment, she retains resolution of double vision and orbital inflammatory signs, and significant improvement in proptosis. She tolerated all infusions with an overall reduction in the severity of her adverse events and without return of significant sensorineural hearing loss. The authors conclude that a lower dose of teprotumumab can be effective for patients with active moderate-severe thyroid eye disease who experience significant or intolerable adverse events.

  View details for DOI 10.1097/IOP.0000000000002355

  View details for PubMedID 36877549

• TDP-43 Proteinopathy in Retina of Chronic Traumatic Encephalopathy Patients Phansalkar, R., Nirschl, J., Goodwill, V., De Lillo, C., Choi, J., Coughlin, D., Pizzo, D., Sigurdson, C., Hiniker, A., Alvarez, V., Mckee, A., Lin, J. ELSEVIER SCIENCE INC. 2023: S1475

  View details for Web of Science ID 000990969803172

• Endocardium-to-coronary artery differentiation during heart development and regeneration involves sequential roles of Bmp2 and Cxcl12/Cxcr4. Developmental cell D'Amato, G., Phansalkar, R., Naftaly, J. A., Fan, X., Amir, Z. A., Rios Coronado, P. E., Cowley, D. O., Quinn, K. E., Sharma, B., Caron, K. M., Vigilante, A., Red-Horse, K. 2022

  Abstract

  Endocardial cells lining the heart lumen are coronary vessel progenitors during embryogenesis. Re-igniting this developmental process in adults could regenerate blood vessels lost during cardiac injury, but this requires additional knowledge of molecular mechanisms. Here, we use mouse genetics and scRNA-seq to identify regulators of endocardial angiogenesis and precisely assess the role of CXCL12/CXCR4 signaling. Time-specific lineage tracing demonstrated that endocardial cells differentiated into coronary endothelial cells primarily at mid-gestation. A new mouse line reporting CXCR4 activity-along with cell-specific gene deletions-demonstrated it was specifically required for artery morphogenesis rather than angiogenesis. Integrating scRNA-seq data of endocardial-derived coronary vessels from mid- and late-gestation identified a Bmp2-expressing transitioning population specific to mid-gestation. Bmp2 stimulated endocardial angiogenesis in vitro and in injured neonatal mouse hearts. Our data demonstrate how understanding the molecular mechanisms underlying endocardial angiogenesis can identify new potential therapeutic targets promoting revascularization of the injured heart.

  View details for DOI 10.1016/j.devcel.2022.10.007

  View details for PubMedID 36347256

• A new resource for human coronary vessel development. Cardiovascular research Phansalkar, R., Red-Horse, K. 2022

  View details for DOI 10.1093/cvr/cvac094

  View details for PubMedID 35726909

• The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science (New York, N.Y.) Jones, R. C., Karkanias, J., Krasnow, M. A., Pisco, A. O., Quake, S. R., Salzman, J., Yosef, N., Bulthaup, B., Brown, P., Harper, W., Hemenez, M., Ponnusamy, R., Salehi, A., Sanagavarapu, B. A., Spallino, E., Aaron, K. A., Concepcion, W., Gardner, J. M., Kelly, B., Neidlinger, N., Wang, Z., Crasta, S., Kolluru, S., Morri, M., Pisco, A. O., Tan, S. Y., Travaglini, K. J., Xu, C., Alcántara-Hernández, M., Almanzar, N., Antony, J., Beyersdorf, B., Burhan, D., Calcuttawala, K., Carter, M. M., Chan, C. K., Chang, C. A., Chang, S., Colville, A., Crasta, S., Culver, R. N., Cvijović, I., D'Amato, G., Ezran, C., Galdos, F. X., Gillich, A., Goodyer, W. R., Hang, Y., Hayashi, A., Houshdaran, S., Huang, X., Irwin, J. C., Jang, S., Juanico, J. V., Kershner, A. M., Kim, S., Kiss, B., Kolluru, S., Kong, W., Kumar, M. E., Kuo, A. H., Leylek, R., Li, B., Loeb, G. B., Lu, W. J., Mantri, S., Markovic, M., McAlpine, P. L., de Morree, A., Morri, M., Mrouj, K., Mukherjee, S., Muser, T., Neuhöfer, P., Nguyen, T. D., Perez, K., Phansalkar, R., Pisco, A. O., Puluca, N., Qi, Z., Rao, P., Raquer-McKay, H., Schaum, N., Scott, B., Seddighzadeh, B., Segal, J., Sen, S., Sikandar, S., Spencer, S. P., Steffes, L. C., Subramaniam, V. R., Swarup, A., Swift, M., Travaglini, K. J., Van Treuren, W., Trimm, E., Veizades, S., Vijayakumar, S., Vo, K. C., Vorperian, S. K., Wang, W., Weinstein, H. N., Winkler, J., Wu, T. T., Xie, J., Yung, A. R., Zhang, Y., Detweiler, A. M., Mekonen, H., Neff, N. F., Sit, R. V., Tan, M., Yan, J., Bean, G. R., Charu, V., Forgó, E., Martin, B. A., Ozawa, M. G., Silva, O., Tan, S. Y., Toland, A., Vemuri, V. N., Afik, S., Awayan, K., Botvinnik, O. B., Byrne, A., Chen, M., Dehghannasiri, R., Detweiler, A. M., Gayoso, A., Granados, A. A., Li, Q., Mahmoudabadi, G., McGeever, A., de Morree, A., Olivieri, J. E., Park, M., Pisco, A. O., Ravikumar, N., Salzman, J., Stanley, G., Swift, M., Tan, M., Tan, W., Tarashansky, A. J., Vanheusden, R., Vorperian, S. K., Wang, P., Wang, S., Xing, G., Xu, C., Yosef, N., Alcántara-Hernández, M., Antony, J., Chan, C. K., Chang, C. A., Colville, A., Crasta, S., Culver, R., Dethlefsen, L., Ezran, C., Gillich, A., Hang, Y., Ho, P. Y., Irwin, J. C., Jang, S., Kershner, A. M., Kong, W., Kumar, M. E., Kuo, A. H., Leylek, R., Liu, S., Loeb, G. B., Lu, W. J., Maltzman, J. S., Metzger, R. J., de Morree, A., Neuhöfer, P., Perez, K., Phansalkar, R., Qi, Z., Rao, P., Raquer-McKay, H., Sasagawa, K., Scott, B., Sinha, R., Song, H., Spencer, S. P., Swarup, A., Swift, M., Travaglini, K. J., Trimm, E., Veizades, S., Vijayakumar, S., Wang, B., Wang, W., Winkler, J., Xie, J., Yung, A. R., Artandi, S. E., Beachy, P. A., Clarke, M. F., Giudice, L. C., Huang, F. W., Huang, K. C., Idoyaga, J., Kim, S. K., Krasnow, M., Kuo, C. S., Nguyen, P., Quake, S. R., Rando, T. A., Red-Horse, K., Reiter, J., Relman, D. A., Sonnenburg, J. L., Wang, B., Wu, A., Wu, S. M., Wyss-Coray, T. 2022; 376 (6594): eabl4896

  Abstract

  Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

  View details for DOI 10.1126/science.abl4896

  View details for PubMedID 35549404

• Management of Functional Vision Disorders. Current neurology and neuroscience reports Phansalkar, R., Lockman, A. J., Bansal, S., Moss, H. E. 2022

  Abstract

  PURPOSE OF REVIEW: The purpose of this review is to summarize current approaches to management of functional vision disorder (FVD).RECENT FINDINGS: Several retrospective studies of FVD in both adults and children have shed light on the range of outcomes and the prevalence of psychosocial stressors among FVD patients. While the first line of treatment for FVD is reassurance and education, recent case reports highlight the use of additional treatment modalities including psychotherapy, hypnosis, and transcranial magnetic stimulation in specific cases. Although the epidemiology and diagnosis of functional vision disorder are well described, there is limited evidence supporting treatment modalities. Nevertheless, the majority of patients improve with conservative management including reassurance, education, and appropriate follow-up. Additional approaches such as mental health care referral can be considered in refractory cases.

  View details for DOI 10.1007/s11910-022-01191-w

  View details for PubMedID 35320465

• Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development ELIFE Phansalkar, R., Krieger, J., Zhao, M., Kolluru, S., Jones, R. C., Quake, S. R., Weissman, I., Bernstein, D., Winn, V. D., D'Amato, G., Red-Horse, K. 2021; 10

  View details for DOI 10.7554/eLife.70246.sa2

  View details for Web of Science ID 000730934300001

• Endocardial/endothelial angiocrines regulate cardiomyocyte development and maturation and induce features of ventricular non-compaction. European heart journal Rhee, S., Paik, D. T., Yang, J. Y., Nagelberg, D., Williams, I., Tian, L., Roth, R., Chandy, M., Ban, J., Belbachir, N., Kim, S., Zhang, H., Phansalkar, R., Wong, K. M., King, D. A., Valdez, C., Winn, V. D., Morrison, A. J., Wu, J. C., Red-Horse, K. 2021

  Abstract

  AIMS: Non-compaction cardiomyopathy is a devastating genetic disease caused by insufficient consolidation of ventricular wall muscle that can result in inadequate cardiac performance. Despite being the third most common cardiomyopathy, the mechanisms underlying the disease, including the cell types involved, are poorly understood. We have previously shown that endothelial cell-specific deletion of the chromatin remodeller gene Ino80 results in defective coronary vessel development that leads to ventricular non-compaction in embryonic mouse hearts. We aimed to identify candidate angiocrines expressed by endocardial and ECs inwildtype and LVNC conditions in Tie2Cre;Ino80fl/fl transgenic embryonic mouse hearts, and test the effect of these candidates on cardiomyocyte proliferation and maturation.METHODS AND RESULTS: We used single-cell RNA-sequencing to characterize endothelial and endocardial defects in Ino80-deficient hearts. We observed a pathological endocardial cell population in the non-compacted hearts and identified multiple dysregulated angiocrine factors that dramatically affected cardiomyocyte behaviour. We identified Col15A1 as a coronary vessel-secreted angiocrine factor, downregulated by Ino80-deficiency, that functioned to promote cardiomyocyte proliferation. Furthermore, mutant endocardial and endothelial cells (ECs) up-regulated expression of secreted factors, such as Tgfbi, Igfbp3, Isg15, and Adm, which decreased cardiomyocyte proliferation and increased maturation.CONCLUSIONS: These findings support a model where coronary ECs normally promote myocardial compaction through secreted factors, but that endocardial and ECs can secrete factors that contribute to non-compaction under pathological conditions.

  View details for DOI 10.1093/eurheartj/ehab298

  View details for PubMedID 34279605

• Dach1 Extends Artery Networks and Protects Against Cardiac Injury. Circulation research Raftrey, B., Williams, I. M., Rios Coronado, P. E., Fan, X., Chang, A. H., Zhao, M., Roth, R. K., Trimm, E., Racelis, R., D'Amato, G., Phansalkar, R., Nguyen, A., Chai, T., Gonzalez, K. M., Zhang, Y., Ang, L. T., Loh, K., Bernstein, D., Red-Horse, K. 2021

  Abstract

  Rationale: Coronary artery disease (CAD) is the leading cause of death worldwide, but there are currently no methods to stimulate artery growth or regeneration in diseased hearts. Studying how arteries are built during development could illuminate strategies for re-building these vessels during ischemic heart disease. We previously found that Dach1 deletion in mouse embryos resulted in small coronary arteries. However, it was not known whether Dach1 gain-of-function would be sufficient to increase arterial vessels and whether this could benefit injury responses. Objective: We investigated how Dach1 overexpression in endothelial cells affected transcription and artery differentiation, and how it influenced recovery from myocardial infarction (MI). Methods and Results: Dach1 was genetically overexpressed in coronary endothelial cells (ECs) in either developing or adult hearts using ApjCreER. This increased the length and number of arterial end branches expanded arteries during development, in both the heart and retina, by inducing capillary ECs to differentiate and contribute to growing arteries. Single-cell RNA sequencing (scRNAseq) of ECs undergoing Dach1-induced arterial specification indicated that it potentiated normal artery differentiation, rather than functioning as a master regulator of artery cell fate. ScRNAseq also showed that normal arterial differentiation is accompanied by repression of lipid metabolism genes, which were also repressed by Dach1. In adults, Dach1 overexpression did not cause a statistically significant change artery structure prior to injury, but increased the number of perfused arteries in the injury zone post-MI. Conclusions: Our data demonstrate that increasing Dach1 is a novel method for driving artery specification and extending arterial branches, which could be explored as a means of mitigating the effects of CAD.

  View details for DOI 10.1161/CIRCRESAHA.120.318271

  View details for PubMedID 34383559

• Single-cell maps of the human heart NATURE Phansalkar, R., Red-Horse, K. 2020; 577 (7792): 629–30

  View details for Web of Science ID 000510520700040

  View details for PubMedID 31988406

• A Unique Collateral Artery Development Program Promotes Neonatal Heart Regeneration CELL Das, S., Goldstone, A. B., Wang, H., Farry, J., D'Amato, G., Paulsen, M. J., Eskandari, A., Hironaka, C. E., Phansalkar, R., Sharma, B., Rhee, S., Shamskhou, E., Agalliu, D., Perez, V., Woo, Y., Red-Horse, K. 2019; 176 (5): 1128-+

  View details for DOI 10.1016/j.cell.2018.12.023

  View details for Web of Science ID 000459257500015