Liya Xu, PhD

Title(s)Assistant Professor
SchoolKeck School of Medicine of Usc
Address4640 West Sunset Blvd
Off Campus
Los Angeles CA 90027
Phone+1 213 740 9945
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    Collapse Biography 
    Collapse Awards and Honors
    Knight Templar Eye Foundation (KTEF)2021Pediatric Ophthalmology Career-Starter Research Grant

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    Collapse Overview
    Liya Xu received her PhD in Neuroscience from University of Southern California 2010. Subsequently, she joined Biomedical Pioneering Innovation Center (BIOPIC) of Peking University to lead the development of one-step next generation sequencing (NGS) based Preimplantation Genetic Diagnosis (PGD) for simultaneous avoidance of monogenic disease and chromosome abnormality. Since 2017, her collaboration with Dr. Jesse Berry has been focusing on developing aqueous humor (AH) as a surrogate tumor biopsy for retinoblastoma (RB). It holds the potential to unlock a new era of precision medicine that will transform the way to detect RB, guide the management and prognosis for RB and lead to alternative treatment regimens that offer a personalized approach to medicine for these children with a greater chance of saving the eye.

    Dr. Xu’s research concentrates on integrating patient, model system, and high-content single particle data to translate clinically observed correlations into a mechanistic understanding of the physical and biological underpinning of the dynamics of ocular cancers, specifically retinoblastoma. Two complementary research projects address the laboratory’s aims of 1) developing the clinical utility of aqueous humors (AH) as liquid biopsy platform for ocular cancer management; and 2) characterizing the tumor circulome of aqueous humor from RB eyes with multi-omics approaches.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Isolation and Characterization of Extracellular Vesicles Through Orthogonal Approaches for the Development of Intraocular EV Therapy. Invest Ophthalmol Vis Sci. 2024 Mar 05; 65(3):6. Leung J, Pollalis D, Nair GKG, Bailey JK, Pennington BO, Khan AI, Kelly KR, Yeh AK, Sundaram KS, Clegg DO, Peng CC, Xu L, Lee SY. PMID: 38466285; PMCID: PMC10929743.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Correlating somatic copy number alteration in aqueous humour cfDNA with chemotherapy history, eye salvage and pathological features in retinoblastoma. Br J Ophthalmol. 2024 02 21; 108(3):449-456. Luo Y, Xu M, Yang L, Yao Y, Berry JL, Xu L, Wen X, He X, Han M, Fan X, Fan J, Jia R. PMID: 36931696; PMCID: PMC10505245.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    3. Aqueous Humor Liquid Biopsy as a Companion Diagnostic for Retinoblastoma: Implications for Diagnosis, Prognosis, and Therapeutic Options: Five Years of Progress. Am J Ophthalmol. 2023 Nov 30; 263:188-205. Berry JL, Pike S, Shah R, Reid MW, Peng CC, Wang Y, Yellapantula V, Biegel J, Kuhn P, Hicks J, Xu L. PMID: 38040321.
      View in: PubMed   Mentions:    Fields:    
    4. Multicentre analysis of nucleic acid quantification using aqueous humour liquid biopsy in uveal melanoma: implications for clinical testing. Can J Ophthalmol. 2023 Nov 27. Pike SB, Reid MW, Peng CC, Chang C, Xu BY, Gombos DS, Patel S, Xu L, Berry JL. PMID: 38036045.
      View in: PubMed   Mentions:    Fields:    
    5. Simultaneous Copy Number Alteration and Single-Nucleotide Variation Analysis in Matched Aqueous Humor and Tumor Samples in Children with Retinoblastoma. Int J Mol Sci. 2023 May 11; 24(10). Schmidt MJ, Prabakar RK, Pike S, Yellapantula V, Peng CC, Kuhn P, Hicks J, Xu L, Berry JL. PMID: 37239954; PMCID: PMC10218537.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    6. Diagnostic Aqueous Humor Proteome Predicts Metastatic Potential in Uveal Melanoma. Int J Mol Sci. 2023 Apr 06; 24(7). Peng CC, Sirivolu S, Pike S, Kim ME, Reiser B, Li HT, Liang G, Xu L, Berry JL. PMID: 37047796; PMCID: PMC10094875.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    7. Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study. J Mol Diagn. 2023 03; 25(3):143-155. Hernandez KM, Bramlett KS, Agius P, Baden J, Cao R, Clement O, Corner AS, Craft J, Dean DA, Dry JR, Grigaityte K, Grossman RL, Hicks J, Higa N, Holzer TR, Jensen J, Johann DJ, Katz S, Kolatkar A, Keynton JL, Lee JSH, Maar D, Martini JF, Meyer CG, Roberts PC, Ryder M, Salvatore L, Schageman JJ, Somiari S, Stetson D, Stern M, Xu L, Leiman LC. PMID: 36828596.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    8. Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors. NPJ Precis Oncol. 2023 Feb 20; 7(1):21. Christodoulou E, Yellapantula V, O'Halloran K, Xu L, Berry JL, Cotter JA, Zdanowicz A, Mascarenhas L, Amatruda JF, Ostrow D, Bootwalla M, Gai X, Navid F, Biegel JA. PMID: 36805676; PMCID: PMC9941464.
      View in: PubMed   Mentions: 3  
    9. A Multicenter Analysis of Nucleic Acid Quantification Using Aqueous Humor Liquid Biopsy in Retinoblastoma: Implications for Clinical Testing. Ophthalmol Sci. 2023 Sep; 3(3):100289. 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. PMID: 37025945; PMCID: PMC10070901.
      View in: PubMed   Mentions: 5  
    10. Non-synonymous, synonymous, and non-coding nucleotide variants contribute to recurrently altered biological processes during retinoblastoma progression. Genes Chromosomes Cancer. 2023 05; 62(5):275-289. Stachelek K, Harutyunyan N, Lee S, Beck A, Kim J, Xu L, Berry JL, Nagiel A, Reynolds CP, Murphree AL, Lee TC, Aparicio JG, Cobrinik D. PMID: 36550020; PMCID: PMC10006380.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    11. Chromosome 6p amplification detected in blood cell-free DNA in advanced intraocular retinoblastoma. Ophthalmic Genet. 2022 12; 43(6):866-870. Sirivolu S, Xu L, Warren M, Prabakar RK, Shah R, Kuhn P, Hicks J, Berry JL. PMID: 36342106; PMCID: PMC9877166.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    12. Malignant teratoid intraocular ciliary body medulloepithelioma in a 5-year-old male with corresponding somatic copy number alteration profile of aqueous humor cell-free DNA. Ophthalmic Genet. 2022 12; 43(6):855-861. Pike S, Iyengar R, Peng CC, Chevez-Barrios P, Brown B, Shah R, Biegel J, Yellapantula V, Nagiel A, Reiser BJ, Xu L, Berry JL. PMID: 36314385; PMCID: PMC9877122.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    13. Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy. Nat Commun. 2022 09 21; 13(1):5523. Li HT, Xu L, Weisenberger DJ, Li M, Zhou W, Peng CC, Stachelek K, Cobrinik D, Liang G, Berry JL. PMID: 36130950; PMCID: PMC9492718.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    14. Identification of epithelial and mesenchymal circulating tumor cells in clonal lineage of an aggressive prostate cancer case. NPJ Precis Oncol. 2022 Jun 21; 6(1):41. Chai S, Ruiz-Velasco C, Naghdloo A, Pore M, Singh M, Matsumoto N, Kolatkar A, Xu L, Shishido S, Aparicio A, Zurita AJ, Hicks J, Kuhn P. PMID: 35729213; PMCID: PMC9213535.
      View in: PubMed   Mentions: 4  
    15. Disease characterization in liquid biopsy from HER2-mutated, non-amplified metastatic breast cancer patients treated with neratinib. NPJ Breast Cancer. 2022 Feb 18; 8(1):22. Shishido SN, Masson R, Xu L, Welter L, Prabakar RK, D' Souza A, Spicer D, Kang I, Jayachandran P, Hicks J, Lu J, Kuhn P. PMID: 35181666; PMCID: PMC8857263.
      View in: PubMed   Mentions: 6  
    16. Aqueous Humor as a Liquid Biopsy for Retinoblastoma: Clear Corneal Paracentesis and Genomic Analysis. J Vis Exp. 2021 09 07; (175). Kim ME, Xu L, Prabakar RK, Shen L, Peng CC, Kuhn P, Gai X, Hicks J, Berry JL. PMID: 34570090; PMCID: PMC9200366.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    17. Treatment response and tumor evolution: lessons from an extended series of multianalyte liquid biopsies in a metastatic breast cancer patient. Cold Spring Harb Mol Case Stud. 2020 12; 6(6). Welter L, Xu L, McKinley D, Dago AE, Prabakar RK, Restrepo-Vassalli S, Xu K, Rodriguez-Lee M, Kolatkar A, Nevarez R, Ruiz C, Nieva J, Kuhn P, Hicks J. PMID: 33203646; PMCID: PMC7784493.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    18. Author Correction: SMURF-seq: efficient copy number profiling on long-read sequencers. Genome Biol. 2020 Aug 25; 21(1):214. Prabakar RK, Xu L, Hicks J, Smith AD. PMID: 32843071; PMCID: PMC7447571.
      View in: PubMed   Mentions:    Fields:    
    19. Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. J Mol Diagn. 2020 03; 22(3):319-337. Shishido SN, Welter L, Rodriguez-Lee M, Kolatkar A, Xu L, Ruiz C, Gerdtsson AS, Restrepo-Vassalli S, Carlsson A, Larsen J, Greenspan EJ, Hwang ES, Waitman KR, Nieva J, Bethel K, Hicks J, Kuhn P. PMID: 31978562; PMCID: PMC7103765.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    20. Aqueous Humor Is Superior to Blood as a Liquid Biopsy for Retinoblastoma. Ophthalmology. 2020 04; 127(4):552-554. Berry JL, Xu L, Polski A, Jubran R, Kuhn P, Kim JW, Hicks J. PMID: 31767439; PMCID: PMC7093221.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    21. SMURF-seq: efficient copy number profiling on long-read sequencers. Genome Biol. 2019 07 08; 20(1):134. Prabakar RK, Xu L, Hicks J, Smith AD. PMID: 31287019; PMCID: PMC6615205.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    22. Genomic cfDNA Analysis of Aqueous Humor in Retinoblastoma Predicts Eye Salvage: The Surrogate Tumor Biopsy for Retinoblastoma. Mol Cancer Res. 2018 11; 16(11):1701-1712. Berry JL, Xu L, Kooi I, Murphree AL, Prabakar RK, Reid M, Stachelek K, Le BHA, Welter L, Reiser BJ, Chévez-Barrios P, Jubran R, Lee TC, Kim JW, Kuhn P, Cobrinik D, Hicks J. PMID: 30061186; PMCID: PMC6214755.
      View in: PubMed   Mentions: 52     Fields:    Translation:Humans
    23. Functional role of the intracellular loop linking transmembrane domains 6 and 7 of the human dipeptide transporter hPEPT1. J Membr Biol. 2010 Dec; 238(1-3):43-9. Xu L, Li Y, Haworth IS, Davies DL. PMID: 21104182; PMCID: PMC3032433.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    24. Mutagenesis and cysteine scanning of transmembrane domain 10 of the human dipeptide transporter. Pharm Res. 2009 Oct; 26(10):2358-66. Xu L, Haworth IS, Kulkarni AA, Bolger MB, Davies DL. PMID: 19685173; PMCID: PMC2861424.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    25. Ethanol inhibits functional activity of the human intestinal dipeptide transporter hPepT1 expressed in Xenopus oocytes. Alcohol Clin Exp Res. 2008 May; 32(5):777-84. Li K, Xu L, Kulkarni AA, Perkins DI, Haworth IS, Davies DL. PMID: 18336632; PMCID: PMC2861421.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
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