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Nesselbush MC, Luca BA, Jeon YJ, Jabara I, Meador CB, Garofalo A, Binkley MS, Hui AB, van 't Erve I, Xu N, Shi WY, Liu KJ, Sugio T, Kastelowitz N, Hamilton EG, Liu CL, Olsen M, Bonilla RF, Wang YP, Jiang A, Lau B, Eichholz J, Banwait M, Schroers-Martin J, Boegeholz J, King DA, Luikart H, Esfahani MS, Mehrmohamadi M, Stehr H, Raclin T, Tibshirani R, Khush K, Srinivas S, Yu H, Rogers AJ, Nair VS, Isbell JM, Li BT, Piotrowska Z, Sequist LV, Hata AN, Neal JW, Wakelee HA, Gentles AJ, Alizadeh AA, Diehn M. An ultrasensitive method for detection of cell-free RNA. Nature 2025; 641:759-768. [PMID: 40240612 DOI: 10.1038/s41586-025-08834-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/24/2025] [Indexed: 04/18/2025]
Abstract
Sensitive methods for detection of cell-free RNA (cfRNA) could facilitate non-invasive gene expression profiling and monitoring of diseases1-6. Here we describe RARE-seq (random priming and affinity capture of cfRNA fragments for enrichment analysis by sequencing), a method optimized for cfRNA analysis. We demonstrate that platelet contamination can substantially confound cfRNA analyses and develop an approach to overcome it. In analytical validations, we find RARE-seq to be approximately 50-fold more sensitive for detecting tumour-derived cfRNA than whole-transcriptome RNA sequencing (RNA-seq), with a limit of detection of 0.05%. To explore clinical utility, we profiled 437 plasma samples from 369 individuals with cancer or non-malignant conditions and controls. Detection of non-small-cell lung cancer expression signatures in cfRNA increased with stage (6 out of 20 (30%) in stage I; 5 out of 8 (63%) in stage II; 10 out of 15 (67%) in stage III; 80 out of 96 (83% sensitivity) in stage IV at 95% specificity) and RARE-seq was more sensitive than tumour-naive circulating tumour DNA (ctDNA) analysis. In patients with EGFR-mutant non-small-cell lung cancer who developed resistance to tyrosine kinase inhibitors, we detected both histological transformation and mutation-based resistance mechanisms. Finally, we demonstrate the potential utility of RARE-seq for determination of tissue of origin, assessing benign pulmonary conditions and tracking response to mRNA vaccines. These results highlight the potential value of ultrasensitive cfRNA analysis and provide proof of concept for diverse clinical applications.
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Affiliation(s)
- Monica C Nesselbush
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Bogdan A Luca
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Young-Jun Jeon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Isabel Jabara
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Catherine B Meador
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrea Garofalo
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Michael S Binkley
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Iris van 't Erve
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Nova Xu
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - William Y Shi
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Kevin J Liu
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Takeshi Sugio
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Noah Kastelowitz
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Emily G Hamilton
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Mari Olsen
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Rene F Bonilla
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Yi Peng Wang
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Alice Jiang
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Brianna Lau
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Jordan Eichholz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mandeep Banwait
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph Schroers-Martin
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Jan Boegeholz
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Daniel A King
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Helen Luikart
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Mohammad S Esfahani
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Henning Stehr
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Tyler Raclin
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Robert Tibshirani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kiran Khush
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Sandy Srinivas
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Helena Yu
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela J Rogers
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Viswam S Nair
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Pulmonary, Critical Care & Sleep Medicine, University of Washington, Seattle, WA, USA
| | - James M Isbell
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T Li
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zofia Piotrowska
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Aaron N Hata
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Joel W Neal
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Heather A Wakelee
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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Shan L, Qiao Y, Ma L, Zhang X, Chen C, Xu X, Li D, Qiu S, Xue X, Yu Y, Guo Y, Qian K, Wang J. AuNPs/CNC Nanocomposite with A "Dual Dispersion" Effect for LDI-TOF MS Analysis of Intact Proteins in NSCLC Serum Exosomes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307360. [PMID: 38224220 DOI: 10.1002/advs.202307360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/07/2023] [Indexed: 01/16/2024]
Abstract
Detecting exosomal markers using laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS) is a novel approach for examining liquid biopsies of non-small cell lung cancer (NSCLC) samples. However, LDI-TOF MS is limited by low sensitivity and poor reproducibility when analyzing intact proteins directly. In this report, gold nanoparticles/cellulose nanocrystals (AuNPs/CNC) is introduced as the matrix for direct analysis of intact proteins in NSCLC serum exosomes. AuNPs/CNC with "dual dispersion" effects dispersed and stabilized AuNPs and improved ion inhibition effects caused by protein aggregation. These features increased the signal-to-noise ratio of [M+H]+ peaks by two orders of magnitude and lowered the detection limit of intact proteins to 0.01 mg mL-1. The coefficient of variation with or without AuNPs/CNC is measured as 10.2% and 32.5%, respectively. The excellent reproducibility yielded a linear relationship (y = 15.41x - 7.983, R2 = 0.989) over the protein concentration range of 0.01 to 20 mg mL-1. Finally, AuNPs/CNC-assisted LDI-TOF MS provides clinically relevant fingerprint information of exosomal proteins in NSCLC serum, and characteristic proteins S100 calcium-binding protein A10, Urokinase plasminogen activator surface receptor, Plasma protease C1 inhibitor, Tyrosine-protein kinase Fgr and Mannose-binding lectin associated serine protease 2 represented excellent predictive biomarkers of NSCLC risk.
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Affiliation(s)
- Liang Shan
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
| | - Yongxia Qiao
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227, South Chongqing Road, Shanghai, 200025, P. R. China
| | - Lifang Ma
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
| | - Changqiang Chen
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
| | - Xin Xu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
| | - Dan Li
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
| | - Shiyu Qiu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
| | - Xiangfei Xue
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
| | - Yongchun Yu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
| | - Yinlong Guo
- National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No. 345, Lingling Road, Shanghai, 200032, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, No. 1954, Huashan Road, Shanghai, 200030, P. R. China
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Road, Shanghai, 200030, P. R. China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, No. 227, South Chongqing Road, Shanghai, 200025, P. R. China
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