1
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Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz JS, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA, Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet AH, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, De Vlaminck I. Plasma cell-free RNA signatures of inflammatory syndromes in children. Proc Natl Acad Sci U S A 2024; 121:e2403897121. [PMID: 39240972 DOI: 10.1073/pnas.2403897121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/25/2024] [Indexed: 09/08/2024] Open
Abstract
Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating cell-free RNA (cfRNA) in plasma as an analyte for the differential diagnosis and characterization of pediatric inflammatory syndromes. We profiled cfRNA in 370 plasma samples from pediatric patients with a range of inflammatory conditions, including Kawasaki disease (KD), multisystem inflammatory syndrome in children (MIS-C), viral infections, and bacterial infections. We developed machine learning models based on these cfRNA profiles, which effectively differentiated KD from MIS-C-two conditions presenting with overlapping symptoms-with high performance [test area under the curve = 0.98]. We further extended this methodology into a multiclass machine learning framework that achieved 80% accuracy in distinguishing among KD, MIS-C, viral, and bacterial infections. We further demonstrated that cfRNA profiles can be used to quantify injury to specific tissues and organs, including the liver, heart, endothelium, nervous system, and the upper respiratory tract. Overall, this study identified cfRNA as a versatile analyte for the differential diagnosis and characterization of a wide range of pediatric inflammatory syndromes.
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Affiliation(s)
- Conor J Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | | | - Andrew Bliss
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
| | - Joan S Lenz
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
| | - Emma Belcher
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
| | - Will Suslovic
- Division of Pediatric Infectious Disease, Children's National Hospital, Washington, DC 20010
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | - Meagan E Williams
- Division of Pediatric Infectious Disease, Children's National Hospital, Washington, DC 20010
| | - Miriam Oseguera
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | - Michael A Gardiner
- Department of Pediatrics, Rady Children's Hospital-San Diego, San Diego, CA 92123
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Jong-Ha Choi
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30307
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Hui-Mien Hsiao
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30307
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Hao Wang
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Jihoon Kim
- Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT 06510
| | - Chisato Shimizu
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Adriana H Tremoulet
- Department of Pediatrics, Rady Children's Hospital-San Diego, San Diego, CA 92123
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Meghan Delaney
- Division of Pediatric Infectious Disease, Children's National Hospital, Washington, DC 20010
- Department of Pediatrics, George Washington University, School of Medicine & Health Sciences, Washington, DC 20052
| | - Roberta L DeBiasi
- Division of Pediatric Infectious Disease, Children's National Hospital, Washington, DC 20010
- Department of Pediatrics, George Washington University, School of Medicine & Health Sciences, Washington, DC 20052
| | - Christina A Rostad
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30307
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Jane C Burns
- Department of Pediatrics, Rady Children's Hospital-San Diego, San Diego, CA 92123
- Department of Pediatrics, Kawasaki Disease Research Center, University of California San Diego, La Jolla, CA 92093
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA 94158
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850
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Zhong P, Bai L, Hong M, Ouyang J, Wang R, Zhang X, Chen P. A Comprehensive Review on Circulating cfRNA in Plasma: Implications for Disease Diagnosis and Beyond. Diagnostics (Basel) 2024; 14:1045. [PMID: 38786343 PMCID: PMC11119755 DOI: 10.3390/diagnostics14101045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Circulating cfRNA in plasma has emerged as a fascinating area of research with potential applications in disease diagnosis, monitoring, and personalized medicine. Circulating RNA sequencing technology allows for the non-invasive collection of important information about the expression of target genes, eliminating the need for biopsies. This comprehensive review aims to provide a detailed overview of the current knowledge and advancements in the study of plasma cfRNA, focusing on its diverse landscape and biological functions, detection methods, its diagnostic and prognostic potential in various diseases, challenges, and future perspectives.
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Affiliation(s)
- Pengqiang Zhong
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Lu Bai
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Mengzhi Hong
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Juan Ouyang
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Ruizhi Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaoli Zhang
- Department of Pediatrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Peisong Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
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3
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Loy C, Cheng MP, Gonzalez-Bocco IH, Lenz J, Belcher E, Bliss A, Eweis-LaBolle D, Chu T, Ritz J, De Vlaminck I. Cell-free RNA Liquid Biopsy to Monitor Hematopoietic Stem Cell Transplantation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307448. [PMID: 38798589 PMCID: PMC11118637 DOI: 10.1101/2024.05.15.24307448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Hematopoietic Stem Cell Transplantation (HSCT) is one of the oldest and most successful immunotherapies. Yet, despite long-standing success in the use of HSCT for the treatment of blood cancers and severe immune disorders, monitoring post-transplant complications remains a challenge due to a lack of informative diagnostic tests. Here, we investigate the utility of cell-free RNA (cfRNA) in plasma as a liquid biopsy to monitor allogeneic HSCT recipients during and after treatment. We assayed longitudinal samples from 92 HSCT recipients by cfRNA sequencing and show that cfRNA provides insight into treatment and recovery trajectories, immune dynamics in response to transplantation, infection, and solid-tissue injury associated with Graft-Versus-Host Disease. Collectively, our results provide support for the use of plasma cfRNA profiling to monitor complications of HSCT.
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Affiliation(s)
- Conor Loy
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, 14853, USA
| | - Matthew P. Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, 02215, USA
- Division of Infectious Disease, Brigham and Women’s Hospital; Boston, 02215, USA
| | - Isabel H. Gonzalez-Bocco
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, 02215, USA
- Division of Infectious Disease, Brigham and Women’s Hospital; Boston, 02215, USA
| | - Joan Lenz
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
| | - Emma Belcher
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
| | - Andrew Bliss
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
| | - Daniel Eweis-LaBolle
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, 14853, USA
| | - Tinyi Chu
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, 02115, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University; Ithaca, 14850, USA
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4
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Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz J, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA, Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet A, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, Vlaminck ID. Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.06.24303645. [PMID: 38496479 PMCID: PMC10942512 DOI: 10.1101/2024.03.06.24303645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating cell-free RNA (cfRNA) in plasma as an analyte for the differential diagnosis and characterization of pediatric inflammatory syndromes. We profiled cfRNA in 370 plasma samples from pediatric patients with a range of inflammatory conditions, including Kawasaki disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), viral infections and bacterial infections. We developed machine learning models based on these cfRNA profiles, which effectively differentiated KD from MIS-C - two conditions presenting with overlapping symptoms - with high performance (Test Area Under the Curve (AUC) = 0.97). We further extended this methodology into a multiclass machine learning framework that achieved 81% accuracy in distinguishing among KD, MIS-C, viral, and bacterial infections. We further demonstrated that cfRNA profiles can be used to quantify injury to specific tissues and organs, including the liver, heart, endothelium, nervous system, and the upper respiratory tract. Overall, this study identified cfRNA as a versatile analyte for the differential diagnosis and characterization of a wide range of pediatric inflammatory syndromes.
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