Cell-Free DNA Tumor Fraction in the Aqueous Humor Is Associated With Therapeutic Response in Retinoblastoma Patients
Ashley Polski, Liya Xu, Rishvanth K Prabakar, Jonathan W Kim, Rachana Shah, Rima Jubran, Peter Kuhn, David Cobrinik, James Hicks, Jesse L Berry, Ashley Polski, Liya Xu, Rishvanth K Prabakar, Jonathan W Kim, Rachana Shah, Rima Jubran, Peter Kuhn, David Cobrinik, James Hicks, Jesse L Berry
Abstract
Purpose: The aqueous humor (AH) liquid biopsy enables in vivo evaluation of tumor-derived cell-free DNA (cfDNA) from retinoblastoma (RB) eyes. Herein, we test our hypothesis that longitudinal dynamics of AH cfDNA-including tumor fraction (TFx) and somatic copy number alteration (SCNA) amplitude-correspond to therapeutic response.
Methods: Eyes with ≥3 AH extractions during intravitreal chemotherapy (IVM) or at secondary enucleation between 2015 to 2019 were included. AH cfDNA was sequenced to assess RB SCNA amplitude; ichorCNA software was used to estimate TFx. Eyes without SCNAs or with TFx < 0.10 across all samples were excluded. Therapeutic responses for each eye were determined from clinical records. Statistical analyses included Mann-Whitney U and Pearson correlation tests.
Results: Twenty eyes of 20 patients underwent ≥3 AH extractions; 6 eyes lacked SCNAs or had TFx < 0.10 throughout sampling and were excluded. Clinical progression was associated with significantly higher SCNA amplitudes and TFx values than regression (P ≤ 0.04). Relative increases in TFx (ΔTFx 1.86 ± 2.22) were associated with disease progression, whereas relative decreases in TFx (ΔTFx 0.53 ± 0.36) were associated with disease regression (P < 0.00001). A ≥15% increase in TFx relative to baseline during treatment was associated with an over 90-fold increased likelihood of clinical progression (odds ratio = 90.67, 95% confidence interval = 8.30-990.16, P = 0.0002). TFx and SCNA amplitude were significantly positively correlated throughout sampling (P ≤ 0.002).
Conclusions: Longitudinal changes in AH-derived cfDNA TFx and SCNA amplitude are concordant with clinical responses of intraocular RB during active therapy.
Translational relevance: Longitudinal evaluation of AH cfDNA may provide an objective, quantitative way to monitor therapeutic response and disease burden in RB patients.
Keywords: aqueous humor; liquid biopsy; retinoblastoma; somatic copy number alteration; tumor fraction.
Conflict of interest statement
Disclosure: A. Polski, None; L. Xu, Aqueous Humor Cell Free DNA for Diagnostic and Prognostic Evaluation of Ophthalmic Disease (P); R.K. Prabakar, None; J.W. Kim, None; R. Shah, None; R. Jubran, None; P. Kuhn, None; D. Cobrinik, None; J. Hicks, Aqueous Humor Cell Free DNA for Diagnostic and Prognostic Evaluation of Ophthalmic Disease (P); J.L. Berry, Aqueous Humor Cell Free DNA for Diagnostic and Prognostic Evaluation of Ophthalmic Disease (P)
Copyright 2020 The Authors.
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References
- Shields JA, Shields CL, Ehya H, Eagle RC, De Potter P. Fine-needle aspiration biopsy of suspected intraocular tumors. The 1992 Urwick Lecture. Ophthalmology. 1993; 100: 1677–1684.
- Karcioglu ZA. Fine needle aspiration biopsy (FNAB) for retinoblastoma. Retina. 2002; 22: 707–710.
- Karcioglu ZA, Gordon RA, Karcioglu GL. Tumor seeding in ocular fine needle aspiration biopsy. Ophthalmology. 1985; 92: 1763–1767.
- Eide N, Syrdalen P, Walaas L, Hagmar B. Fine needle aspiration biopsy in selecting treatment for inconclusive intraocular disease. Acta Ophthalmol Scand. 1999; 77: 448–452.
- Eide N, Walaas L.. Fine-needle aspiration biopsy and other biopsies in suspected intraocular malignant disease: a review. Acta Ophthalmol. 2009; 87: 588–601.
- Eriksson O, Hagmar B, Ryd W. Effects of fine-needle aspiration and other biopsy procedures on tumor dissemination in mice. Cancer. 1984; 54: 73–78.
- Ali MJ, Honavar SG, Vemuganti GK, Singh AD. Fine needle aspiration biopsy of retinal tumors. Monogr Clin Cytol. 2012; 21: 72–81.
- Berry JL, Xu L, Kooi I, et al. .. Genomic cfDNA analysis of aqueous humor in retinoblastoma predicts eye salvage: the surrogate tumor biopsy for retinoblastoma. Mol Cancer Res. 2018; 16: 1701–1712.
- Berry JL, Xu L, Murphree AL, et al. .. Potential of aqueous humor as a surrogate tumor biopsy for retinoblastoma. JAMA Ophthalmol. 2017; 135: 1221–1230.
- Berry JL, Xu L, Polski A, et al. .. Aqueous humor is superior to blood as a liquid biopsy for retinoblastoma. Ophthalmology. 2020; 127: 552–554.
- Lianidou E, Pantel K. Liquid biopsies. Genes Chromosomes Cancer. 2019; 58: 219–232.
- Choudhury AD, Werner L, Francini E, et al. .. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight. 2018; 3: e122109.
- Chen X, Chang CW, Spoerke JM, et al. .. Low-pass whole-genome sequencing of circulating cell-free DNA demonstrates dynamic changes in genomic copy number in a squamous lung cancer clinical cohort. Clin Cancer Res. 2019; 25: 2254–2263.
- Oellerich M, Schütz E, Beck J, et al. .. Using circulating cell-free DNA to monitor personalized cancer therapy. Crit Rev Clin Lab Sci. 2017; 54: 205–218.
- Tissot C, Toffart AC, Villar S, et al. .. Circulating free DNA concentration is an independent prognostic biomarker in lung cancer. Eur Respir J. 2015; 46: 1773–1780.
- Stover DG, Parsons HA, Ha G, et al. .. Association of cell-free DNA tumor fraction and somatic copy number alterations with survival in metastatic triple-negative breast cancer. J Clin Oncol. 2018; 36: 543–553.
- Berry JL, Jubran R, Kim JW, et al. .. Long-term outcomes of Group D eyes in bilateral retinoblastoma patients treated with chemoreduction and low-dose IMRT salvage. Pediatr Blood Cancer. 2013; 60: 688–693.
- Berry JL, Shah S, Bechtold M, Zolfaghari E, Jubran R, Kim JW. Long-term outcomes of Group D retinoblastoma eyes during the intravitreal melphalan era. Pediatr Blood Cancer. 2017; 64.
- Munier FL, Soliman S, Moulin AP, Gaillard MC, Balmer A, Beck-Popovic M. Profiling safety of intravitreal injections for retinoblastoma using an anti-reflux procedure and sterilisation of the needle track. Br J Ophthalmol. 2012; 96: 1084–1087.
- Baslan T, Kendall J, Rodgers L, et al. .. Genome-wide copy number analysis of single cells. Nat Protoc. 2012; 7: 1024–1041.
- Baslan T, Kendall J, Rodgers L, et al. .. Corrigendum: Genome-wide copy number analysis of single cells. Nat Protoc. 2016; 11: 616.
- Corson TW, Gallie BL. One hit, two hits, three hits, more? Genomic changes in the development of retinoblastoma. Genes Chromosomes Cancer. 2007; 46: 617–634.
- Adalsteinsson VA, Ha G, Freeman SS, et al. .. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun. 2017; 8: 1324.
- Murphree A.L. The case for a new group classification of intraocular retinoblastoma. Ophthalmol Clin North Am. 2005; 18: 41–53.
- Mallipatna A., et al. . In: Amin MB, Edge SB, Greene FL, eds. AJCC Cancer Staging Manual Vol. 8th Edition. Ch. 68, Springer; 2017: 819–831.
- Ghassemi F, Amoli FA.. Pathological findings in enucleated eyes after intravitreal melphalan injection. Int Ophthalmol. 2014; 34: 533–540.
- Rushlow DE, Mol BM, Kennett JY, et al. .. Characterisation of retinoblastomas without RB1 mutations: genomic, gene expression, and clinical studies. Lancet Oncol. 2013; 14: 327–334.
- Gerrish A, Stone E, Clokie S, et al. .. Non-invasive diagnosis of retinoblastoma using cell-free DNA from aqueous humour. Br J Ophthalmol. 2019; 103: 721–724.
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