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Im DH, Pike S, Reid MW, Peng CC, Sirivolu S, Grossniklaus HE, Hubbard GB, Skalet AH, Bellsmith KN, Shields CL, Lally SE, Stacey AW, Reiser BJ, Nagiel A, Shah R, Xu L, Berry JL. A multicenter analysis of nucleic acid quantification using aqueous humor liquid biopsy in retinoblastoma – Implications for clinical testing. Ophthalmology Science 2023; 3:100289. [PMID: 37025945 PMCID: PMC10070901 DOI: 10.1016/j.xops.2023.100289] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
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 Disclosures Proprietary or commercial disclosure may be found after the references.
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Affiliation(s)
- Deborah H. Im
- 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
- 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
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
| | - Chen-Ching Peng
- 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
- 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
| | | | - G. Baker Hubbard
- Emory Eye Center, Emory University School of Medicine, Atlanta, Georgia
| | - Alison H. Skalet
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
| | - Kellyn N. Bellsmith
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
| | - Carol L. Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Sara E. Lally
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Andrew W. Stacey
- Division of Ophthalmology, Department of Ophthalmology, Seattle Children’s Hospital, University of Washington, Seattle, Washington
| | - Bibiana J. Reiser
- 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
- 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
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, California
| | - Liya Xu
- 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
- 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.
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Im DH, Peng CC, Xu L, Kim ME, Ostrow D, Yellapantula V, Bootwalla M, Biegel JA, Gai X, Prabakar RK, Kuhn P, Hicks J, Berry JL. Potential of Aqueous Humor as a Liquid Biopsy for Uveal Melanoma. Int J Mol Sci 2022; 23:ijms23116226. [PMID: 35682905 PMCID: PMC9181140 DOI: 10.3390/ijms23116226] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022] Open
Abstract
Tumor biopsy can identify prognostic biomarkers for metastatic uveal melanoma (UM), however aqueous humor (AH) liquid biopsy may serve as an adjunct. This study investigated whether the AH of UM eyes has sufficient circulating tumor DNA (ctDNA) to perform genetic analysis. This is a case series of 37 AH samples, taken before or after radiation, and one tumor wash sample, from 12 choroidal and 8 ciliary body (CB) melanoma eyes. AH was analyzed for nucleic acid concentrations. AH DNA and one tumor wash sample underwent shallow whole-genome sequencing followed by Illumina sequencing to detect somatic copy number alterations (SCNAs). Four post-radiation AH underwent targeted sequencing of BAP1 and GNAQ genes. Post-radiation AH had significantly higher DNA and miRNA concentrations than paired pre-radiation samples. Highly recurrent UM SCNAs were identified in 0/11 post-radiation choroidal and 6/8 post-radiation CB AH. SCNAs were highly concordant in a CB post-radiation AH with its matched tumor (r = 0.978). BAP1 or GNAQ variants were detected in 3/4 post-radiation AH samples. AH is a source of ctDNA in UM eyes, particularly in post-radiation CB eyes. For the first time, UM SCNAs and mutations were identified in AH-derived ctDNA. Suggesting that AH can serve as a liquid biopsy for UM.
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Affiliation(s)
- Deborah H. Im
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.H.I.); (C.-C.P.); (L.X.); (M.E.K.)
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chen-Ching Peng
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.H.I.); (C.-C.P.); (L.X.); (M.E.K.)
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Liya Xu
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.H.I.); (C.-C.P.); (L.X.); (M.E.K.)
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mary E. Kim
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.H.I.); (C.-C.P.); (L.X.); (M.E.K.)
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Dejerianne Ostrow
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.O.); (V.Y.); (M.B.); (J.A.B.); (X.G.)
| | - Venkata Yellapantula
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.O.); (V.Y.); (M.B.); (J.A.B.); (X.G.)
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Moiz Bootwalla
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.O.); (V.Y.); (M.B.); (J.A.B.); (X.G.)
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Jaclyn A. Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.O.); (V.Y.); (M.B.); (J.A.B.); (X.G.)
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.O.); (V.Y.); (M.B.); (J.A.B.); (X.G.)
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Rishvanth K. Prabakar
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (R.K.P.); (P.K.); (J.H.)
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (R.K.P.); (P.K.); (J.H.)
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (R.K.P.); (P.K.); (J.H.)
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jesse L. Berry
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (D.H.I.); (C.-C.P.); (L.X.); (M.E.K.)
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
- Correspondence:
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Abstract
Multiple dose administration of methamphetamine (MA) results in long-lasting toxic effects in the nigrostriatal dopaminergic system. These effects are considered to be primarily due to oxidative damage mediated by increased production of hydrogen peroxide or other reactive oxygen species in the dopaminergic system. The present study was designed to determine the protective effects of dietary antioxidant selenium on MA-induced neurotoxicity in the nigrostriatal dopaminergic system. Male C57BL/6J mice were fed either selenium-deficient (< 0.01 ppm Se) or selenium-replete (0.2 ppm Se) diets for 90 days. MA treatment decreased the dopamine (DA) levels in the striatum and substantia nigra (SN) of both Se-replete and Se-deficient animals. However, in Se-replete animals, this DA depletion was significantly attenuated in both the striatum and SN. A novel observation is that MA administration resulted in increased activity of Cu,Zn-SOD in the brains of both Se-deficient and Se-replete animals. However, MA administration to Se-deficient animals exhibited a higher Cu,Zn-SOD activity in the nigrostriatal system than the control animals. Elevated malondialdehyde (MDA) levels in the striatum and SN were also observed in Se-deficient MA-treated animals. Se repletion significantly increased the glutathione peroxidase (GPx) activity and the ratio of reduced glutathione (GSH)/oxidized glutathione (GSSG) in the MA-treated animals. In conclusion, we have shown that dietary Se attenuated methamphetamine neurotoxicity and that this protection involves GPx-mediated antioxidant mechanisms. Even though Cu,Zn-SOD activity was significantly elevated by MA treatment, the role of this enzyme in MA-mediated neurotoxicity is not yet clear.
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Affiliation(s)
- H C Kim
- Department of Pharmacy, College of Pharmacy, Kangwon National University, Korea Institute of Drug Abuse, Chunchon, South Korea.
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