A Multicenter Analysis of Nucleic Acid Quantification Using Aqueous Humor Liquid Biopsy in Retinoblastoma

Deborah H. Im, BS; Sarah Pike, BA; Mark W. Reid, PhD; Chen-Ching Peng, PhD; Shreya Sirivolu, BA; Hans E. Grossniklaus, MD, MBA; G. Baker Hubbard, 3rd, MD; Alison H. Skalet, MD, PhD; Kellyn N. Bellsmith, MD; Carol L. Shields, MD; Sara E. Lally, MD; Andrew W. Stacey, MD; Bibiana J. Reiser, MD; Aaron Nagiel, MD, PhD; Rachana Shah, MD; Liya Xu, PhD; Jesse L. Berry, MD

Ophthalmology Science (Sep 2023)

A Multicenter Analysis of Nucleic Acid Quantification Using Aqueous Humor Liquid Biopsy in Retinoblastoma

Deborah H. Im, BS,
Sarah Pike, BA,
Mark W. Reid, PhD,
Chen-Ching Peng, PhD,
Shreya Sirivolu, BA,
Hans E. Grossniklaus, MD, MBA,
G. Baker Hubbard, 3rd, MD,
Alison H. Skalet, MD, PhD,
Kellyn N. Bellsmith, MD,
Carol L. Shields, MD,
Sara E. Lally, MD,
Andrew W. Stacey, MD,
Bibiana J. Reiser, MD,
Aaron Nagiel, MD, PhD,
Rachana Shah, MD,
Liya Xu, PhD,
Jesse L. Berry, MD

Affiliations

Deborah H. Im, BS: Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California; USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
Sarah Pike, BA: Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California; USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
Mark W. Reid, PhD: Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
Chen-Ching Peng, PhD: Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California; USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
Shreya Sirivolu, BA: Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California; USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
Hans E. Grossniklaus, MD, MBA: Emory Eye Center, Emory University School of Medicine, Atlanta, Georgia
G. Baker Hubbard, 3rd, MD: Emory Eye Center, Emory University School of Medicine, Atlanta, Georgia
Alison H. Skalet, MD, PhD: Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
Kellyn N. Bellsmith, MD: Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
Carol L. Shields, MD: Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
Sara E. Lally, MD: Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
Andrew W. Stacey, MD: Division of Ophthalmology, Department of Ophthalmology, Seattle Children’s Hospital, University of Washington, Seattle, Washington
Bibiana J. Reiser, MD: Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California; USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
Aaron Nagiel, MD, PhD: Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California; USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
Rachana Shah, MD: Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, California
Liya Xu, PhD: Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California; USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
Jesse L. Berry, MD: Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California; USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California; The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, California; Correspondence: Jesse L. Berry, MD, Director of Ocular Oncology, Children’s Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA 90027.

Journal volume & issue: Vol. 3, no. 3
p. 100289

Abstract

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Purpose: Retinoblastoma (RB) is most often diagnosed with clinical features and not diagnosed with tumor biopsy. This study describes tumor-derived analyte concentrations from aqueous humor (AH) liquid biopsy and its use in clinical assays. Design: Case series study. Participants: Sixty-two RB eyes from 55 children and 14 control eyes from 12 children from 4 medical centers. Methods: This study included 128 RB AH samples including: diagnostic (DX) samples, samples from eyes undergoing treatment (TX), samples after completing treatment (END), and during bevacizumab injection for radiation therapy after completing RB treatment (BEV). Fourteen-control AH were analyzed for unprocessed analytes (double-stranded DNA [dsDNA], single-stranded DNA [ssDNA], micro-RNA [miRNA], RNA, and protein) with Qubit fluorescence assays. Double-stranded DNA from 2 RB AH samples underwent low-pass whole-genome sequencing to detect somatic copy number alterations. Logistic regression was used to predict disease burden given analyte concentrations. Main Outcome Measures: Unprocessed analyte (dsDNA, ssDNA, miRNA, RNA and protein) concentrations. Results: Results revealed dsDNA, ssDNA, miRNA, and proteins, but not RNA, were quantifiable in most samples (up to 98%) with Qubit fluorescence assays. Median dsDNA concentration was significantly higher in DX (3.08 ng/μl) compared to TX (0.18 ng/μl; P < 0.0001) at an order of 17 times greater and 20 times greater than END samples (0.15 ng/μl; P = 0.001). Using logistic regression, nucleic acid concentrations were useful in predicting higher versus lower RB disease burden. Retinoblastoma somatic copy number alterations were identified in a TX, but not in a BEV sample, indicating the correlation with RB activity. Conclusions: Aqueous humor liquid biopsy in RB is a high-yield source of dsDNA, ssDNA, miRNA, and protein. Diagnostic samples are most useful for RB 1 gene mutational analyses. Genomic analysis may be more informative of tumor activity status than quantification alone and can be performed even with smaller analyte concentrations obtained from TX samples. Financial Disclosure(s): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Published in Ophthalmology Science

ISSN: 2666-9145 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Medicine: Ophthalmology
Website: https://www.journals.elsevier.com/ophthalmology-science/

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