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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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2
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De Sota RE, Quake SR, Sninsky JJ, Toden S. Decoding bioactive signals of the RNA secretome: the cell-free messenger RNA catalogue. Expert Rev Mol Med 2024; 26:e12. [PMID: 38682644 PMCID: PMC11140549 DOI: 10.1017/erm.2024.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/18/2024] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
Despite gene-expression profiling being one of the most common methods to evaluate molecular dysregulation in tissues, the utilization of cell-free messenger RNA (cf-mRNA) as a blood-based non-invasive biomarker analyte has been limited compared to other RNA classes. Recent advancements in low-input RNA-sequencing and normalization techniques, however, have enabled characterization as well as accurate quantification of cf-mRNAs allowing direct pathological insights. The molecular profile of the cell-free transcriptome in multiple diseases has subsequently been characterized including, prenatal diseases, neurological disorders, liver diseases and cancers suggesting this biological compartment may serve as a disease agnostic platform. With mRNAs packaged in a myriad of extracellular vesicles and particles, these signals may be used to develop clinically actionable, non-invasive disease biomarkers. Here, we summarize the recent scientific developments of extracellular mRNA, biology of extracellular mRNA carriers, clinical utility of cf-mRNA as disease biomarkers, as well as proposed functions in cell and tissue pathophysiology.
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Affiliation(s)
- Rhys E. De Sota
- Superfluid Dx., 259 E Grand Avenue, South San Francisco, CA 94080, USA
| | - Stephen R. Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - John J. Sninsky
- Superfluid Dx., 259 E Grand Avenue, South San Francisco, CA 94080, USA
| | - Shusuke Toden
- Superfluid Dx., 259 E Grand Avenue, South San Francisco, CA 94080, USA
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3
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Stanley KE, Jatsenko T, Tuveri S, Sudhakaran D, Lannoo L, Van Calsteren K, de Borre M, Van Parijs I, Van Coillie L, Van Den Bogaert K, De Almeida Toledo R, Lenaerts L, Tejpar S, Punie K, Rengifo LY, Vandenberghe P, Thienpont B, Vermeesch JR. Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology. Nat Commun 2024; 15:2220. [PMID: 38472221 PMCID: PMC10933257 DOI: 10.1038/s41467-024-46435-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell types that release them. Current methods for cfDNA deconvolution typically use disease tailored marker selection in a limited number of bulk tissues or cell lines. Here, we utilize single cell transcriptome data as a comprehensive cellular reference set for disease-agnostic cfDNA cell-of-origin analysis. We correlate cfDNA-inferred nucleosome spacing with gene expression to rank the relative contribution of over 490 cell types to plasma cfDNA. In 744 healthy individuals and patients, we uncover cell type signatures in support of emerging disease paradigms in oncology and prenatal care. We train predictive models that can differentiate patients with colorectal cancer (84.7%), early-stage breast cancer (90.1%), multiple myeloma (AUC 95.0%), and preeclampsia (88.3%) from matched controls. Importantly, our approach performs well in ultra-low coverage cfDNA datasets and can be readily transferred to diverse clinical settings for the expansion of liquid biopsy.
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Affiliation(s)
- Kate E Stanley
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Tatjana Jatsenko
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Stefania Tuveri
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Dhanya Sudhakaran
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Lore Lannoo
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Marie de Borre
- Department of Human Genetics, Laboratory for Functional Epigenetics, KU Leuven, Leuven, Belgium
| | - Ilse Van Parijs
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Van Coillie
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Liesbeth Lenaerts
- Department of Oncology, Gynecological Oncology, KU Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Kevin Punie
- Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Laura Y Rengifo
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, Laboratory for Functional Epigenetics, KU Leuven, Leuven, Belgium
| | - Joris Robert Vermeesch
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium.
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4
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Sun Y, Yu H, Han S, Ran R, Yang Y, Tang Y, Wang Y, Zhang W, Tang H, Fu B, Fu B, Weng X, Liu SM, Deng H, Peng S, Zhou X. Method for the extraction of circulating nucleic acids based on MOF reveals cell-free RNA signatures in liver cancer. Natl Sci Rev 2024; 11:nwae022. [PMID: 38348130 PMCID: PMC10860518 DOI: 10.1093/nsr/nwae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/24/2023] [Accepted: 09/24/2023] [Indexed: 02/15/2024] Open
Abstract
Cell-free RNA (cfRNA) allows assessment of health, status, and phenotype of a variety of human organs and is a potential biomarker to non-invasively diagnose numerous diseases. Nevertheless, there is a lack of highly efficient and bias-free cfRNA isolation technologies due to the low abundance and instability of cfRNA. Here, we developed a reproducible and high-efficiency isolation technology for different types of cell-free nucleic acids (containing cfRNA and viral RNA) in serum/plasma based on the inclusion of nucleic acids by metal-organic framework (MOF) materials, which greatly improved the isolation efficiency and was able to preserve RNA integrity compared with the most widely used research kit method. Importantly, the quality of cfRNA extracted by the MOF method is about 10-fold that of the kit method, and the MOF method isolates more than three times as many different RNA types as the kit method. The whole transcriptome mapping characteristics of cfRNA in serum from patients with liver cancer was described and a cfRNA signature with six cfRNAs was identified to diagnose liver cancer with high diagnostic efficiency (area under curve = 0.905 in the independent validation cohort) using this MOF method. Thus, this new MOF isolation technique will advance the field of liquid biopsy, with the potential to diagnose liver cancer.
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Affiliation(s)
- Yuqing Sun
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Haixin Yu
- Department of Digestive Surgical Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Ruoxi Ran
- Department of Clinical Laboratory, Center for Gene Diagnosis and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Ying Yang
- Department of Clinical Laboratory, Center for Gene Diagnosis and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yongling Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Yuhao Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Wenhao Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Heng Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Boqiao Fu
- College of Chemistry and Materials Science, Hubei Engineering University, Xiaogan 432000, China
| | - Boshi Fu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Hexiang Deng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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5
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Zhou S, Li J, Yang W, Xue P, Yin Y, Wang Y, Tian P, Peng H, Jiang H, Xu W, Huang S, Zhang R, Wei F, Sun HX, Zhang J, Zhao L. Noninvasive preeclampsia prediction using plasma cell-free RNA signatures. Am J Obstet Gynecol 2023; 229:553.e1-553.e16. [PMID: 37211139 DOI: 10.1016/j.ajog.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/02/2023] [Accepted: 05/14/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Preeclampsia, especially preterm preeclampsia and early-onset preeclampsia, is a life-threating pregnancy disorder, and the heterogeneity and complexity of preeclampsia make it difficult to predict risk and to develop treatments. Plasma cell-free RNA carries unique information from human tissue and may be useful for noninvasive monitoring of maternal, placental, and fetal dynamics during pregnancy. OBJECTIVE This study aimed to investigate various RNA biotypes associated with preeclampsia in plasma and to develop classifiers to predict preterm preeclampsia and early-onset preeclampsia before diagnosis. STUDY DESIGN We performed a novel, cell-free RNA sequencing method termed polyadenylation ligation-mediated sequencing to investigate the cell-free RNA characteristics of 715 healthy pregnancies and 202 pregnancies affected by preeclampsia before symptom onset. We explored differences in the abundance of different RNA biotypes in plasma between healthy and preeclampsia samples and built preterm preeclampsia and early-onset preeclampsia prediction classifiers using machine learning methods. Furthermore, we validated the performance of the classifiers using the external and internal validation cohorts and assessed the area under the curve and positive predictive value. RESULTS We detected 77 genes, including messenger RNA (44%) and microRNA (26%), that were differentially expressed in healthy mothers and mothers with preterm preeclampsia before symptom onset, which could separate participants with preterm preeclampsia from healthy samples and that played critical functional roles in preeclampsia physiology. We developed 2 classifiers for predicting preterm preeclampsia and early-onset preeclampsia before diagnosis based on 13 cell-free RNA signatures and 2 clinical features (in vitro fertilization and mean arterial pressure), respectively. Notably, both classifiers showed enhanced performance when compared with the existing methods. The preterm preeclampsia prediction model achieved 81% area under the curve and 68% positive predictive value in an independent validation cohort (preterm, n=46; control, n=151); the early-onset preeclampsia prediction model had an area under the curve of 88% and a positive predictive value of 73% in an external validation cohort (early-onset preeclampsia, n=28; control, n=234). Furthermore, we demonstrated that downregulation of microRNAs may play vital roles in preeclampsia through the upregulation of preeclampsia-relevant target genes. CONCLUSION In this cohort study, a comprehensive transcriptomic landscape of different RNA biotypes in preeclampsia was presented and 2 advanced classifiers with substantial clinical importance for preterm preeclampsia and early-onset preeclampsia prediction before symptom onset were developed. We demonstrated that messenger RNA, microRNA, and long noncoding RNA can simultaneously serve as potential biomarkers of preeclampsia, holding the promise of prevention of preeclampsia in the future. Abnormal cell-free messenger RNA, microRNA, and long noncoding RNA molecular changes may help to elucidate the pathogenic determinants of preeclampsia and open new therapeutic windows to effectively reduce pregnancy complications and fetal morbidity.
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Affiliation(s)
- Si Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; BGI Genomics, BGI-Shenzhen, Shenzhen, China; Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co, Ltd, Shijiazhuang, Hebei Province, China; Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | - Jie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; BGI-Shenzhen, Shenzhen, China; BGI-Beijing, Beijing, China
| | - Wenzhi Yang
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co, Ltd, Shijiazhuang, Hebei Province, China; Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | - Penghao Xue
- Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | - Yanning Yin
- Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | - Yunfang Wang
- Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China
| | | | | | | | - Wenqiu Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shang Huang
- Shenzhen Children's Hospital of China Medical University, Shenzhen, China
| | - Rui Zhang
- Division of Maternal-Fetal Medicine, Jinan University-affiliated Shenzhen Baoan Women's and Children's Hospital, Shenzhen, China.
| | - Fengxiang Wei
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, China.
| | - Hai-Xi Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; BGI-Shenzhen, Shenzhen, China; BGI-Beijing, Beijing, China.
| | - Jianguo Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China; Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co, Ltd, Shijiazhuang, Hebei Province, China; Shijiazhuang BGI Clinical Laboratory Co, Ltd, Shijiazhuang, Hebei Province, China.
| | - Lijian Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China; Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co, Ltd, Shijiazhuang, Hebei Province, China; Medical Technology College of Hebei Medical University, Shijiazhuang, China.
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6
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Vorperian SK, DeFelice BC, Buonomo JA, Chinchinian HJ, Gray IJ, Yan J, Mach KE, La V, Lee TJ, Liao JC, Lafayette R, Loeb GB, Bertozzi CR, Quake SR. Multiomics characterization of cell type repertoires for urine liquid biopsies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563226. [PMID: 37961398 PMCID: PMC10634682 DOI: 10.1101/2023.10.20.563226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Urine is assayed alongside blood in medicine, yet current clinical diagnostic tests utilize only a small fraction of its total biomolecular repertoire, potentially foregoing high-resolution insights into human health and disease. In this work, we characterized the joint landscapes of transcriptomic and metabolomic signals in human urine. We also compared the urine transcriptome to plasma cell-free RNA, identifying a distinct cell type repertoire and enrichment for metabolic signal. Untargeted metabolomic measurements identified a complementary set of pathways to the transcriptomic analysis. Our findings suggest that urine is a promising biofluid yielding prognostic and detailed insights for hard-to-biopsy tissues with low representation in the blood, offering promise for a new generation of liquid biopsies.
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7
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Safrastyan A, Zu Siederdissen CH, Wollny D. Decoding cell-type contributions to the cfRNA transcriptomic landscape of liver cancer. Hum Genomics 2023; 17:90. [PMID: 37798661 PMCID: PMC10552294 DOI: 10.1186/s40246-023-00537-w] [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: 07/26/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Liquid biopsy, particularly cell-free RNA (cfRNA), has emerged as a promising non-invasive diagnostic tool for various diseases, including cancer, due to its accessibility and the wealth of information it provides. A key area of interest is the composition and cellular origin of cfRNA in the blood and the alterations in the cfRNA transcriptomic landscape during carcinogenesis. Investigating these changes can offer insights into the manifestations of tissue alterations in the blood, potentially leading to more effective diagnostic strategies. However, the consistency of these findings across different studies and their clinical utility remains to be fully elucidated, highlighting the need for further research in this area. RESULTS In this study, we analyzed over 350 blood samples from four distinct studies, investigating the cell type contributions to the cfRNA transcriptomic landscape in liver cancer. We found that an increase in hepatocyte proportions in the blood is a consistent feature across most studies and can be effectively utilized for classifying cancer and healthy samples. Moreover, our analysis revealed that in addition to hepatocytes, liver endothelial cell signatures are also prominent in the observed changes. By comparing the classification performance of cellular proportions to established markers, we demonstrated that cellular proportions could distinguish cancer from healthy samples as effectively as existing markers and can even enhance classification when used in combination with these markers. CONCLUSIONS Our comprehensive analysis of liver cell-type composition changes in blood revealed robust effects that help classify cancer from healthy samples. This is especially noteworthy, considering the heterogeneous nature of datasets and the etiological distinctions of samples. Furthermore, the observed differences in results across studies underscore the importance of integrative and comparative approaches in the future research to determine the consistency and robustness of findings. This study contributes to the understanding of cfRNA composition in liver cancer and highlights the potential of cellular deconvolution in liquid biopsy.
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Affiliation(s)
- Aram Safrastyan
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany.
- Leibniz Institute On Aging-Fritz Lipmann Institute (FLI), Jena, Germany.
| | | | - Damian Wollny
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany.
- Leibniz Institute On Aging-Fritz Lipmann Institute (FLI), Jena, Germany.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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8
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Kim HJ, Rames MJ, Goncalves F, Kirschbaum CW, Roskams-Hieter B, Spiliotopoulos E, Briand J, Doe A, Estabrook J, Wagner JT, Demir E, Mills G, Ngo TTM. Selective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesicles. Commun Biol 2023; 6:885. [PMID: 37644220 PMCID: PMC10465482 DOI: 10.1038/s42003-023-05232-z] [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: 10/05/2022] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Extracellular vesicles (EVs) have been shown as key mediators of extracellular small RNA transport. However, carriers of cell-free messenger RNA (cf-mRNA) in human biofluids and their association with cancer remain poorly understood. Here, we performed a transcriptomic analysis of size-fractionated plasma from lung cancer, liver cancer, multiple myeloma, and healthy donors. Morphology and size distribution analysis showed the successful separation of large and medium particles from other soluble plasma protein fractions. We developed a strategy to purify and sequence ultra-low amounts of cf-mRNA from particle and protein enriched subpopulations with the implementation of RNA spike-ins to control for technical variability and to normalize for intrinsic drastic differences in cf-mRNA amount carried in each plasma fraction. We found that the majority of cf-mRNA was enriched and protected in EVs with remarkable stability in RNase-rich environments. We observed specific enrichment patterns of cancer-associated cf-mRNA in each particle and protein enriched subpopulation. The EV-enriched differentiating genes were associated with specific biological pathways, such as immune systems, liver function, and toxic substance regulation in lung cancer, liver cancer, and multiple myeloma, respectively. Our results suggest that dissecting the complexity of EV subpopulations illuminates their biological significance and offers a promising liquid biopsy approach.
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Affiliation(s)
- Hyun Ji Kim
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Matthew J Rames
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Florian Goncalves
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - C Ward Kirschbaum
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Breeshey Roskams-Hieter
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Elias Spiliotopoulos
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Josephine Briand
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Aaron Doe
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Joseph Estabrook
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA
| | - Josiah T Wagner
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Molecular Genomics Laboratory, Providence Health and Services, Portland, OR, USA
| | - Emek Demir
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Gordon Mills
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Thuy T M Ngo
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
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9
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Liu Y, Liang Y, Li Q, Li Q. Comprehensive analysis of circulating cell-free RNAs in blood for diagnosing non-small cell lung cancer. Comput Struct Biotechnol J 2023; 21:4238-4251. [PMID: 37692082 PMCID: PMC10491804 DOI: 10.1016/j.csbj.2023.08.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023] Open
Abstract
Early screening and detection of non-small cell lung cancer (NSCLC) is crucial due to the significantly low survival rate in advanced stages. Blood-based liquid biopsy is non-invasive test to assistant disease diagnosis, while cell-free RNA is one of the promising biomarkers in blood. However, the disease related signatures have not been explored completely for most cell-free RNA transcriptome sequencing (cfRNA-Seq) datasets. To address this gap, we developed a comprehensive cfRNA-Seq pipeline for data analysis and constructed a machine learning model to facilitate noninvasive early diagnosis of NSCLC. The results of our study have demonstrated the identification of differential mRNA, lncRNAs and miRNAs from cfRNA-Seq, which have exhibited significant association with development and progression of lung cancer. The classifier based on gene expression signatures achieved an impressive area under the curve (AUC) of up to 0.9, indicating high specificity and sensitivity in both cross-validation and independent test. Furthermore, the analysis of T cell and B cell immune repertoire extracted from cfRNA-Seq have provided insights into the immune status of cancer patients, while the microbiome analysis has revealed distinct bacterial and viral profiles between NSCLC and normal samples. In our future work, we aim to validate the existence of cancer associated T cell receptors (TCR)/B cell receptors (BCR) and microorganisms, and subsequently integrate all identified signatures into diagnostic model to improve the prediction accuracy. This study not only provided a comprehensive analysis pipeline for cfRNA-Seq dataset but also highlights the potential of cfRNAs as promising biomarkers and models for early NSCLC diagnosis, emphasizing their importance in clinical settings.
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Affiliation(s)
| | | | - Qiyan Li
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Qingjiao Li
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
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10
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Moufarrej MN, Bianchi DW, Shaw GM, Stevenson DK, Quake SR. Noninvasive Prenatal Testing Using Circulating DNA and RNA: Advances, Challenges, and Possibilities. Annu Rev Biomed Data Sci 2023; 6:397-418. [PMID: 37196360 PMCID: PMC10528197 DOI: 10.1146/annurev-biodatasci-020722-094144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Prenatal screening using sequencing of circulating cell-free DNA has transformed obstetric care over the past decade and significantly reduced the number of invasive diagnostic procedures like amniocentesis for genetic disorders. Nonetheless, emergency care remains the only option for complications like preeclampsia and preterm birth, two of the most prevalent obstetrical syndromes. Advances in noninvasive prenatal testing expand the scope of precision medicine in obstetric care. In this review, we discuss advances, challenges, and possibilities toward the goal of providing proactive, personalized prenatal care. The highlighted advances focus mainly on cell-free nucleic acids; however, we also review research that uses signals from metabolomics, proteomics, intact cells, and the microbiome. We discuss ethical challenges in providing care. Finally, we look to future possibilities, including redefining disease taxonomy and moving from biomarker correlation to biological causation.
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Affiliation(s)
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development and Section on Prenatal Genomics and Fetal Therapy, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gary M Shaw
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - David K Stevenson
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, California, USA
- Chan Zuckerberg Initiative, Redwood City, California, USA
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11
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Loy CJ, Sotomayor-Gonzalez A, Servellita V, Nguyen J, Lenz J, Bhattacharya S, Williams ME, Cheng AP, Bliss A, Saldhi P, Brazer N, Streithorst J, Suslovic W, Hsieh CJ, Bahar B, Wood N, Foresythe A, Gliwa A, Bhakta K, Perez MA, Hussaini L, Anderson EJ, Chahroudi A, Delaney M, Butte AJ, DeBiasi RL, Rostad CA, De Vlaminck I, Chiu CY. Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C. Cell Rep Med 2023; 4:101034. [PMID: 37279751 PMCID: PMC10121104 DOI: 10.1016/j.xcrm.2023.101034] [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: 07/15/2022] [Revised: 11/28/2022] [Accepted: 04/11/2023] [Indexed: 06/08/2023]
Abstract
Differential host responses in coronavirus disease 2019 (COVID-19) and multisystem inflammatory syndrome in children (MIS-C) remain poorly characterized. Here, we use next-generation sequencing to longitudinally analyze blood samples from pediatric patients with COVID-19 or MIS-C across three hospitals. Profiling of plasma cell-free nucleic acids uncovers distinct signatures of cell injury and death between COVID-19 and MIS-C, with increased multiorgan involvement in MIS-C encompassing diverse cell types, including endothelial and neuronal cells, and an enrichment of pyroptosis-related genes. Whole-blood RNA profiling reveals upregulation of similar pro-inflammatory pathways in COVID-19 and MIS-C but also MIS-C-specific downregulation of T cell-associated pathways. Profiling of plasma cell-free RNA and whole-blood RNA in paired samples yields different but complementary signatures for each disease state. Our work provides a systems-level view of immune responses and tissue damage in COVID-19 and MIS-C and informs future development of new disease biomarkers.
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Affiliation(s)
- Conor J Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joan Lenz
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Sanchita Bhattacharya
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Alexandre P Cheng
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Andrew Bliss
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Noah Brazer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jessica Streithorst
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Charlotte J Hsieh
- Division of Pediatric Infectious Diseases and Global Health, Department of Pediatrics, University of California San Francisco, Oakland, CA 94609
| | - Burak Bahar
- Children's National Hospital, Washington, DC 20010, USA
| | - Nathan Wood
- UCSF Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Abiodun Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amelia Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kushmita Bhakta
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Maria A Perez
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Laila Hussaini
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Evan J Anderson
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA; Department of Medicine, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Meghan Delaney
- Children's National Hospital, Washington, DC 20010, USA; The George Washington University School of Medicine, Washington, DC 20052, USA
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Roberta L DeBiasi
- Children's National Hospital, Washington, DC 20010, USA; The George Washington University School of Medicine, Washington, DC 20052, USA
| | - Christina A Rostad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
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12
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Li S, Zhang E, Cai Z. Liquid biopsy by analysis of circulating myeloma cells and cell-free nucleic acids: a novel noninvasive approach of disease evaluation in multiple myeloma. Biomark Res 2023; 11:27. [PMID: 36890597 PMCID: PMC9997021 DOI: 10.1186/s40364-023-00469-6] [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: 12/20/2022] [Accepted: 02/26/2023] [Indexed: 03/10/2023] Open
Abstract
Multiple myeloma (MM) is an incurable hematological cancer with high spatial- and temporal-heterogeneity. Invasive single-point bone marrow sampling cannot capture the tumor heterogeneity and is difficult to repeat for serial assessments. Liquid biopsy is a technique for identifying and analyzing circulating MM cells and cell products produced by tumors and released into the circulation, allowing for the minimally invasive and comprehensive detection of disease burden and molecular alterations in MM and monitoring treatment response and disease progression. Furthermore, liquid biopsy can provide complementary information to conventional detection approaches and improve their prognostic values. This article reviewed the technologies and applications of liquid biopsy in MM.
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Affiliation(s)
- Shuchan Li
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, No. 79, Qingchun Road, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Enfan Zhang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, No. 79, Qingchun Road, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Cai
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, No. 79, Qingchun Road, Hangzhou, Zhejiang, China. .,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.
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13
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Schroers-Martin JG, Alig S, Garofalo A, Tessoulin B, Sugio T, Alizadeh AA. Molecular Monitoring of Lymphomas. ANNUAL REVIEW OF PATHOLOGY 2023; 18:149-180. [PMID: 36130071 DOI: 10.1146/annurev-pathol-050520-044652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Molecular monitoring of tumor-derived alterations has an established role in the surveillance of leukemias, and emerging nucleic acid sequencing technologies are likely to similarly transform the clinical management of lymphomas. Lymphomas are well suited for molecular surveillance due to relatively high cell-free DNA and circulating tumor DNA concentrations, high somatic mutational burden, and the existence of stereotyped variants enabling focused interrogation of recurrently altered regions. Here, we review the clinical scenarios and key technologies applicable for the molecular monitoring of lymphomas, summarizing current evidence in the literature regarding molecular subtyping and classification, evaluation of treatment response, the surveillance of active cellular therapies, and emerging clinical trial strategies.
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Affiliation(s)
- Joseph G Schroers-Martin
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA;
| | - Stefan Alig
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA;
| | - Andrea Garofalo
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA;
| | - Benoit Tessoulin
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA; .,Current affiliation: Clinical Hematology Department, Nantes University Hospital, Nantes, France
| | - Takeshi Sugio
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA;
| | - Ash A Alizadeh
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA; .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA.,Stanford Cancer Institute, Stanford University, Stanford, California, USA
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14
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Chaddha M, Rai H, Gupta R, Thakral D. Integrated analysis of circulating cell free nucleic acids for cancer genotyping and immune phenotyping of tumor microenvironment. Front Genet 2023; 14:1138625. [PMID: 37091783 PMCID: PMC10117686 DOI: 10.3389/fgene.2023.1138625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/15/2023] [Indexed: 04/25/2023] Open
Abstract
The circulating cell-free nucleic acids (ccfNAs) consist of a heterogenous cocktail of both single (ssNA) and double-stranded (dsNA) nucleic acids. These ccfNAs are secreted into the blood circulation by both healthy and malignant cells via various mechanisms including apoptosis, necrosis, and active secretion. The major source of ccfNAs are the cells of hematopoietic system under healthy conditions. These ccfNAs include fragmented circulating cell free DNA (ccfDNA), coding or messenger RNA (mRNA), long non-coding RNA (lncRNA), microRNA (miRNA), and mitochondrial DNA/RNA (mtDNA and mtRNA), that serve as prospective biomarkers in assessment of various clinical conditions. For, e.g., free fetal DNA and RNA migrate into the maternal plasma, whereas circulating tumor DNA (ctDNA) has clinical relevance in diagnostic, prognostic, therapeutic targeting, and disease progression monitoring to improve precision medicine in cancer. The epigenetic modifications of ccfDNA as well as circulating cell-free RNA (ccfRNA) such as miRNA and lncRNA show disease-related variations and hold potential as epigenetic biomarkers. The messenger RNA present in the circulation or the circulating cell free mRNA (ccf-mRNA) and long non-coding RNA (ccf-lncRNA) have gradually become substantial in liquid biopsy by acting as effective biomarkers to assess various aspects of disease diagnosis and prognosis. Conversely, the simultaneous characterization of coding and non-coding RNAs in human biofluids still poses a significant hurdle. Moreover, a comprehensive assessment of ccfRNA that may reflect the tumor microenvironment is being explored. In this review, we focus on the novel approaches for exploring ccfDNA and ccfRNAs, specifically ccf-mRNA as biomarkers in clinical diagnosis and prognosis of cancer. Integrating the detection of circulating tumor DNA (ctDNA) for cancer genotyping in conjunction with ccfRNA both quantitatively and qualitatively, may potentially hold immense promise towards precision medicine. The current challenges and future directions in deciphering the complexity of cancer networks based on the dynamic state of ccfNAs will be discussed.
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Affiliation(s)
| | | | - Ritu Gupta
- *Correspondence: Deepshi Thakral, ; Ritu Gupta,
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15
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Albrecht LJ, Höwner A, Griewank K, Lueong SS, von Neuhoff N, Horn PA, Sucker A, Paschen A, Livingstone E, Ugurel S, Zimmer L, Horn S, Siveke JT, Schadendorf D, Váraljai R, Roesch A. Circulating cell-free messenger RNA enables non-invasive pan-tumour monitoring of melanoma therapy independent of the mutational genotype. Clin Transl Med 2022; 12:e1090. [PMID: 36320118 PMCID: PMC9626658 DOI: 10.1002/ctm2.1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/09/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Plasma-derived tumour-specific cell-free nucleic acids are increasingly utilized as a minimally invasive, real-time biomarker approach in many solid tumours. Circulating tumour DNA of melanoma-specific mutations is currently the best studied liquid biopsy biomarker for melanoma. However, the combination of hotspot genetic alterations covers only around 80% of all melanoma patients. Therefore, alternative approaches are needed to enable the follow-up of all genotypes, including wild-type. METHODS We identified KPNA2, DTL, BACE2 and DTYMK messenger RNA (mRNA) upregulated in melanoma versus nevi tissues by unsupervised data mining (N = 175 melanoma, N = 20 normal skin, N = 6 benign nevi) and experimentally confirmed differential mRNA expression in vitro (N = 18 melanoma, N = 8 benign nevi). Circulating cell-free RNA (cfRNA) was analysed in 361 plasma samples (collected before and during therapy) from 100 melanoma patients and 18 healthy donors. Absolute cfRNA copies were quantified on droplet digital PCR. RESULTS KPNA2, DTL, BACE2 and DTYMK cfRNA demonstrated high diagnostic accuracy between melanoma patients' and healthy donors' plasma (AUC > 86%, p < .0001). cfRNA copies increased proportionally with increasing tumour burden independently of demographic variables and even remained elevated in individuals with radiological absence of disease. Re-analysis of single-cell transcriptomes revealed a pan-tumour origin of cfRNA, including endothelial, cancer-associated fibroblasts, macrophages and B cells beyond melanoma cells as cellular sources. Low baseline cfRNA levels were associated with significantly longer progression-free survival (PFS) (KPNA2 HR = .54, p = .0362; DTL HR = .60, p = .0349) and overall survival (KPNA2 HR = .52, p = .0237; BACE2 HR = .55, p = .0419; DTYMK HR = .43, p = .0393). Lastly, we found that cfRNA copies significantly increased during therapy in non-responders compared to responders regardless of therapy and mutational subtypes and that the increase of KPNA2 (HR = 1.73, p = .0441) and DTYMK (HR = 1.82, p = .018) cfRNA during therapy was predictive of shorter PFS. CONCLUSIONS In sum, we identified a new panel of cfRNAs for a pan-tumour liquid biopsy approach and demonstrated its utility as a prognostic, therapy-monitoring tool independent of the melanoma mutational genotype.
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Affiliation(s)
- Lea Jessica Albrecht
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Anna Höwner
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Klaus Griewank
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Smiths S. Lueong
- Bridge Institute of Experimental Tumor TherapyWest German Cancer CenterUniversity Hospital of EssenUniversity of Duisburg‐EssenEssenGermany
- Division of Solid Tumor Translational OncologyGerman Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research CenterDKFZHeidelbergGermany
| | - Nils von Neuhoff
- Department of Pediatric Hematology and OncologyDepartment for Pediatrics IIIUniversity Hospital of EssenEssenGermany
| | - Peter A. Horn
- Institute for Transfusion MedicineUniversity Hospital of EssenEssenGermany
| | - Antje Sucker
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Annette Paschen
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Elisabeth Livingstone
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Selma Ugurel
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Lisa Zimmer
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Susanne Horn
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
- Faculty Rudolf‐Schönheimer‐Institute for BiochemistryUniversity of LeipzigLeipzigGermany
| | - Jens T. Siveke
- Bridge Institute of Experimental Tumor TherapyWest German Cancer CenterUniversity Hospital of EssenUniversity of Duisburg‐EssenEssenGermany
- Division of Solid Tumor Translational OncologyGerman Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research CenterDKFZHeidelbergGermany
| | - Dirk Schadendorf
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Renáta Váraljai
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Alexander Roesch
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
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16
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Qi J, Wu B, Chen X, Wei W, Yao X. Diagnostic biomolecules and combination therapy for pre-eclampsia. Reprod Biol Endocrinol 2022; 20:136. [PMID: 36068569 PMCID: PMC9446775 DOI: 10.1186/s12958-022-01003-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Pre-eclampsia (PE), associated with placental malperfusion, is the primary reason for maternal and perinatal mortality and morbidity that can cause vascular endothelial injury and multi-organ injury. Despite considerable research efforts, no pharmaceutical has been shown to stop disease progression. If women precisely diagnosed with PE can achieve treatment at early gestation, the maternal and fetal outcomes can be maximally optimized by expectant management. Current diagnostic approaches applying maternal characteristics or biophysical markers, including blood test, urine analysis and biophysical profile, possess limitations in the precise diagnosis of PE. Biochemical factor research associated with PE development has generated ambitious diagnostic targets based on PE pathogenesis and dissecting molecular phenotypes. This review focuses on current developments in biochemical prediction of PE and the corresponding interventions to ameliorate disease progression, aiming to provide references for clinical diagnoses and treatments.
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Affiliation(s)
- Jingqi Qi
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, No. N1, Shangcheng Avenue, Yiwu, 322000, China
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Bingbing Wu
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, No. N1, Shangcheng Avenue, Yiwu, 322000, China
| | - Xiuying Chen
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, No. N1, Shangcheng Avenue, Yiwu, 322000, China
| | - Wei Wei
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, No. N1, Shangcheng Avenue, Yiwu, 322000, China.
| | - Xudong Yao
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, No. N1, Shangcheng Avenue, Yiwu, 322000, China.
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17
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Zhuang J, Ibarra A, Acosta A, Karns AP, Aballi J, Nerenberg M, Sninsky JJ, Quake SR, Toden S. Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice. EBioMedicine 2022; 83:104242. [PMID: 36054939 PMCID: PMC9437808 DOI: 10.1016/j.ebiom.2022.104242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
Background Inflammatory and immune responses are essential and dynamic biological processes that protect the body against acute and chronic adverse stimuli. While conventional protein markers have been used to evaluate systemic inflammatory response, the immunological response to stimulation is complex and involves modulation of a large set of genes and interacting signalling pathways of innate and adaptive immune systems. There is a need for a non-invasive tool that can comprehensively evaluate and monitor molecular dysregulations associated with inflammatory and immune responses in circulation and in inaccessible solid organs. Methods Here we utilized cell-free messenger RNA (cf-mRNA) RNA-Seq whole transcriptome profiling and computational biology to temporally assess lipopolysaccharide (LPS) induced and JAK inhibitor modulated inflammatory and immune responses in mouse plasma samples. Findings Cf-mRNA profiling displayed a pattern of systemic immune responses elicited by LPS and dysregulation of associated pathways. Moreover, attenuation of several inflammatory pathways, including STAT and interferon pathways, were observed following the treatment of JAK inhibitor. We further identified the dysregulation of liver-specific transcripts in cf-mRNA which reflected changes in the gene-expression pattern in this generally inaccessible biological compartment. Interpretation Using a preclinical mouse model, we demonstrated the potential of plasma cf-mRNA profiling for systemic and organ-specific characterization of drug-induced molecular alterations that are associated with inflammatory and immune responses. Funding Molecular Stethoscope.
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Affiliation(s)
- Jiali Zhuang
- Molecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United States
| | - Arkaitz Ibarra
- Molecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United States
| | - Alexander Acosta
- Molecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United States
| | - Amy P Karns
- Molecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United States
| | - Jonathan Aballi
- Molecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United States
| | - Michael Nerenberg
- Molecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United States
| | - John J Sninsky
- Molecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United States
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University and Chan Zuckerberg Biohub, Stanford, CA 94305, United States
| | - Shusuke Toden
- Molecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United States.
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18
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Sun J, Yang X, Wang T, Xing Y, Chen H, Zhu S, Zeng J, Zhou Q, Chen F, Zhang X, Wang WJ. Evaluating the Effects of Storage Conditions on Multiple Cell-Free RNAs in Plasma by High-Throughput Sequencing. Biopreserv Biobank 2022. [PMID: 36006659 DOI: 10.1089/bio.2022.0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Plasma cell-free RNAs (cfRNAs) can serve as noninvasive biomarkers for the diagnosis and monitoring of diseases. However, the delay in blood processing may lead to unreliable results. Therefore, an unbiased evaluation based on the whole transcriptome under different storage conditions is needed. Methods: Here, blood samples were collected in ethylenediaminetetraacetic acid tubes and processed immediately (0 hour), or stored at room temperature (RT) or 4°C for different time intervals (2, 6, and 24 hours) before plasma separation. High-throughput sequencing was applied to assess the effects of storage conditions on the transcript profiles and fragment characteristics of plasma cell-free mRNA, long noncoding RNA (lncRNA), and small RNAs. Results: More genes changed their expression levels with time when blood was stored at RT compared with those at 4°C. Cell-free mRNA and lncRNA were relatively stable in blood preserved at 4°C for 6 hours, while cell-free microRNA (miRNA) and piwi-interacting RNA (piRNA) remained stable at 4°C for 24 hours. After 24 hours, more contamination of the leukocyte-derived RNAs occurred at RT, possibly due to apoptosis. Meanwhile, significant changes were also observed regarding the characteristics of the RNA fragments, including fragment size, the proportion of intron, and the pyrimidine frequency of the fragmented 3' end. Fifteen tissue-enriched genes were detected in the plasma but not expressed in leukocytes. The expression level and fragment length of these genes gradually decreased during storage, suggesting the degradation of the cfRNA and the dilution of leukocyte-derived RNA with other tissue-derived cfRNA. Conclusions: Our results suggest that the contamination of leukocyte-derived RNA and the degradation of original cfRNA contribute to the changes in the cfRNA expression profiles and the fragment characteristics during short-term storage. The storage of blood at 4°C for 6 hours allows plasma cfRNA to remain relatively stable, which will be useful for further studies or clinical applications where adequate quantification or the fragment signature of cfRNA is required.
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Affiliation(s)
- Jinghua Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China
| | - Xi Yang
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Sujun Zhu
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Juan Zeng
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | | | | | | | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Engineering Laboratory for Birth Defects Screening, BGI-Shenzhen, Shenzhen, China
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19
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Hassan S, Shehzad A, Khan SA, Miran W, Khan S, Lee YS. Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management. Biomedicines 2022; 10:biomedicines10082047. [PMID: 36009594 PMCID: PMC9405989 DOI: 10.3390/biomedicines10082047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 11/20/2022] Open
Abstract
Over time, molecular biology and genomics techniques have been developed to speed up the early diagnosis and clinical management of cancer. These therapies are often most effective when administered to the subset of malignancies harboring the target identified by molecular testing. Important advances in applying molecular testing involve circulating-free DNA (cfDNA)- and cell-free RNA (cfRNA)-based liquid biopsies for the diagnosis, prognosis, prediction, and treatment of cancer. Both cfDNA and cfRNA are sensitive and specific biomarkers for cancer detection, which have been clinically proven through multiple randomized and prospective trials. These help in cancer management based on the noninvasive evaluation of size, quantity, and point mutations, as well as copy number alterations at the tumor site. Moreover, personalized detection of ctDNA helps in adjuvant therapeutics and predicts the chances of recurrence of cancer and resistance to cancer therapy. Despite the controversial diagnostic values of cfDNA and cfRNA, many clinical trials have been completed, and the Food and Drug Administration has approved many multigene assays to detect genetic alterations in the cfDNA of cancer patients. In this review, we underpin the recent advances in the physiological roles of cfDNA and cfRNA, as well as their roles in cancer detection by highlighting recent clinical trials and their roles as prognostic and predictive markers in cancer management.
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Affiliation(s)
- Sadia Hassan
- Department of Biomedical Engineering and Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Adeeb Shehzad
- Department of Biomedical Engineering and Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
- Correspondence: (A.S.); (Y.-S.L.)
| | - Shahid Ali Khan
- Department of Chemistry, School of Natural Sciences (SNS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Waheed Miran
- Department of Chemical Engineering, School of Chemical and Materials Engineering National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Salman Khan
- Department of pharmacy, Quaid-i-Azam University, Islamabad 44000, Pakistan
| | - Young-Sup Lee
- School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea
- Correspondence: (A.S.); (Y.-S.L.)
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20
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Current challenges and best practices for cell-free long RNA biomarker discovery. Biomark Res 2022; 10:62. [PMID: 35978416 PMCID: PMC9385245 DOI: 10.1186/s40364-022-00409-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
The analysis of biomarkers in biological fluids, also known as liquid biopsies, is seen with great potential to diagnose complex diseases such as cancer with a high sensitivity and minimal invasiveness. Although it can target any biomolecule, most liquid biopsy studies have focused on circulating nucleic acids. Historically, studies have aimed at the detection of specific mutations on cell-free DNA (cfDNA), but recently, the study of cell-free RNA (cfRNA) has gained traction. Since 2020, a handful of cfDNA tests have been approved for therapy selection by the FDA, however, no cfRNA tests are approved to date. One of the main drawbacks in the field of RNA-based liquid biopsies is the low reproducibility of the results, often caused by technical and biological variability, a lack of standardized protocols and insufficient cohorts. In this review, we will identify the main challenges and biases introduced during the different stages of biomarker discovery in liquid biopsies with cfRNA and propose solutions to minimize them.
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21
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Metzenmacher M, Hegedüs B, Forster J, Schramm A, Horn PA, Klein CA, Bielefeld N, Ploenes T, Aigner C, Siveke JT, Schuler M, Lueong SS. The clinical utility of cfRNA for disease detection and surveillance: A proof of concept study in non-small cell lung cancer. Thorac Cancer 2022; 13:2180-2191. [PMID: 35708207 PMCID: PMC9346179 DOI: 10.1111/1759-7714.14540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 12/01/2022] Open
Abstract
Background CT scans are used in routine clinical practice for the diagnosis and treatment surveillance of non‐small cell lung cancer (NSCLC). However, more sensitive methods are desirable. Liquid biopsy analyses of RNA and DNA can offer more sensitive diagnostic approaches. Cell‐free RNA (cfRNA) has been described in several malignancies, but its clinical utility has not previously been explored. Methods We evaluated the clinical utility of cfRNA for early detection and surveillance of tumor disease in a proof‐of‐concept study. Using real‐time‐droplet digital polymerase chain reaction we characterized a candidate transcript (MORF4L2) in plasma samples from 41 advanced stage, 38 early stage NSCLC and 39 healthy samples. We compared its diagnostic performance with tumor markers and evaluated its utility for disease monitoring. Results MORF4L2 cfRNA was more abundant in patients than in healthy donors (p < 0.0001). Using the Youden index approach (cutoff value of 537 copies/ml was established) with a sensitivity of 0.73 (95% CI: 0.61–0.82) and a specificity of 0.87 (95% CI: 0.73–0.96). Positive and negative predictive values of 0.92 (95% CI: 0.83–0.95) and 0.59 (95% CI: 0.47–0.83) were achieved. Combination of cfRNA and Cyfra21‐1 improved its predictive value from 89.5% to 94.7%. Low baseline MORF4L2 levels were associated with better overall survival (HR:0.25, 95% CI: 0.09–0.7, p = 0.009) and progression‐free survival for patients treated with tyrosine kinase inhibitors (p = 0.011) and chemotherapy (p = 0.019). MORF4L2 profile between baseline and follow‐up mirrored radiological response and tumor dynamics better than tumor markers. cfRNA transcripts allowed monitoring tumor dynamics in patients without tumor‐reported genetic alterations. Conclusion Our data support clinical utility of cfRNA for detection and surveillance of NSCLC. Further studies with larger cohorts are required.
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Affiliation(s)
- Martin Metzenmacher
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Thoracic Oncology, West German Cancer Center, University Medicine Essen Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
| | - Balazs Hegedüs
- Department of Thoracic Surgery, West German Cancer Center, University Medicine Essen Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
| | - Jan Forster
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Essen, Germany.,Chair for Genome Informatics, Department of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Alexander Schramm
- Laboratory for Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | - Christoph A Klein
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany.,Fraunhofer-Institute for Toxicology and Experimental Medicine, Division of Personalized Tumor Therapy, Regensburg, Germany
| | - Nicola Bielefeld
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Essen, Germany.,Bridge Institute of Experimental Tumor Therapy, West German Cancer Center and Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK), University Hospital Essen, University Duisburg-Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Till Ploenes
- Department of Thoracic Surgery, West German Cancer Center, University Medicine Essen Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
| | - Clemens Aigner
- Department of Thoracic Surgery, West German Cancer Center, University Medicine Essen Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
| | - Jens T Siveke
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Essen, Germany.,Bridge Institute of Experimental Tumor Therapy, West German Cancer Center and Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK), University Hospital Essen, University Duisburg-Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Martin Schuler
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Thoracic Oncology, West German Cancer Center, University Medicine Essen Ruhrlandklinik, University Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner site University Hospital Essen, Essen, Germany
| | - Smiths S Lueong
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Essen, Germany.,Bridge Institute of Experimental Tumor Therapy, West German Cancer Center and Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK), University Hospital Essen, University Duisburg-Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
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22
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Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies. NPJ Precis Oncol 2022; 6:28. [PMID: 35468987 PMCID: PMC9038724 DOI: 10.1038/s41698-022-00270-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/16/2022] [Indexed: 01/23/2023] Open
Abstract
Cell-free RNA (cfRNA) in plasma reflects phenotypic alterations of both localized sites of cancer and the systemic host response. Here we report that cfRNA sequencing enables the discovery of messenger RNA (mRNA) biomarkers in plasma with the tissue of origin-specific to cancer types and precancerous conditions in both solid and hematologic malignancies. To explore the diagnostic potential of total cfRNA from blood, we sequenced plasma samples of eight hepatocellular carcinoma (HCC) and ten multiple myeloma (MM) patients, 12 patients of their respective precancerous conditions, and 20 non-cancer (NC) donors. We identified distinct gene sets and built classification models using Random Forest and linear discriminant analysis algorithms that could distinguish cancer patients from premalignant conditions and NC individuals with high accuracy. Plasma cfRNA biomarkers of HCC are liver-specific genes and biomarkers of MM are highly expressed in the bone marrow compared to other tissues and are related to cell cycle processes. The cfRNA level of these biomarkers displayed a gradual transition from noncancerous states through precancerous conditions and cancer. Sequencing data were cross-validated by quantitative reverse transcription PCR and cfRNA biomarkers were validated in an independent sample set (20 HCC, 9 MM, and 10 NC) with AUC greater than 0.86. cfRNA results observed in precancerous conditions require further validation. This work demonstrates a proof of principle for using mRNA transcripts in plasma with a small panel of genes to distinguish between cancers, noncancerous states, and precancerous conditions.
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23
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Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui ABY, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol 2022; 40:585-597. [PMID: 35361996 PMCID: PMC9337986 DOI: 10.1038/s41587-022-01222-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
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Affiliation(s)
- Mohammad Shahrokh Esfahani
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Emily G. Hamilton
- Program in Cancer Biology, Stanford School of Medicine, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Stefan K. Alig
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel A. King
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Chloé B. Steen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - Charles W. Macaulay
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | | | - Joanne Soo
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joseph G. Schroers-Martin
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Binbin Chen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Michael S. Binkley
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Brian J. Sworder
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Angela B-Y Hui
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Chih Long Liu
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - James M. Isbell
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M. Kurtz
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| | - Ash A. Alizadeh
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
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24
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LncRNA Biomarkers of Inflammation and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:121-145. [PMID: 35220568 DOI: 10.1007/978-3-030-92034-0_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are promising candidates as biomarkers of inflammation and cancer. LncRNAs have several properties that make them well-suited as molecular markers of disease: (1) many lncRNAs are expressed in a tissue-specific manner, (2) distinct lncRNAs are upregulated based on different inflammatory or oncogenic stimuli, (3) lncRNAs released from cells are packaged and protected in extracellular vesicles, and (4) circulating lncRNAs in the blood are detectable using various RNA sequencing approaches. Here we focus on the potential for lncRNA biomarkers to detect inflammation and cancer, highlighting key biological, technological, and analytical considerations that will help advance the development of lncRNA-based liquid biopsies.
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25
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Abstract
Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases. Cell types affected by various diseases are inferred from cell-free RNA.
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26
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Moufarrej MN, Vorperian SK, Wong RJ, Campos AA, Quaintance CC, Sit RV, Tan M, Detweiler AM, Mekonen H, Neff NF, Baruch-Gravett C, Litch JA, Druzin ML, Winn VD, Shaw GM, Stevenson DK, Quake SR. Early prediction of preeclampsia in pregnancy with cell-free RNA. Nature 2022; 602:689-694. [PMID: 35140405 PMCID: PMC8971130 DOI: 10.1038/s41586-022-04410-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 01/06/2022] [Indexed: 12/30/2022]
Abstract
Liquid biopsies that measure circulating cell-free RNA (cfRNA) offer an opportunity to study the development of pregnancy-related complications in a non-invasive manner and to bridge gaps in clinical care1-4. Here we used 404 blood samples from 199 pregnant mothers to identify and validate cfRNA transcriptomic changes that are associated with preeclampsia, a multi-organ syndrome that is the second largest cause of maternal death globally5. We find that changes in cfRNA gene expression between normotensive and preeclamptic mothers are marked and stable early in gestation, well before the onset of symptoms. These changes are enriched for genes specific to neuromuscular, endothelial and immune cell types and tissues that reflect key aspects of preeclampsia physiology6-9, suggest new hypotheses for disease progression and correlate with maternal organ health. This enabled the identification and independent validation of a panel of 18 genes that when measured between 5 and 16 weeks of gestation can form the basis of a liquid biopsy test that would identify mothers at risk of preeclampsia long before clinical symptoms manifest themselves. Tests based on these observations could help predict and manage who is at risk for preeclampsia-an important objective for obstetric care10,11.
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Affiliation(s)
- Mira N Moufarrej
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sevahn K Vorperian
- ChEM-H and Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ana A Campos
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecele C Quaintance
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rene V Sit
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | | | | | | | - James A Litch
- Global Alliance to Prevent Prematurity and Stillbirth (GAPPS), Lynnwood, WA, USA
| | - Maurice L Druzin
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
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27
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Kiat Whye K, ShyongTai E, Shabbir A, Khoo CM, Koh W. Non-Invasive Characterization of the Pancreas During Bariatric Surgery via Circulating Pancreatic Specific Cell-free Messenger RNA. Front Genet 2021; 12:742496. [PMID: 34707641 PMCID: PMC8542674 DOI: 10.3389/fgene.2021.742496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/10/2021] [Indexed: 11/30/2022] Open
Abstract
Bariatric surgery results in sustained weight loss and improvement in glucose homeostasis. However, the lack of accessible non-invasive tools to examine molecular alterations occurring in the pancreas limits our understanding of the causes and recovery of glucose homeostasis. Here, we describe the use of a circulating cell free mRNA (cfmRNA) based multiplex qPCR assay to selectively amplify and quantify circulating pancreatic specific transcripts levels within plasma. We applied this assay to a cohort of 58 plasma samples consisting of 10 patients that tracks multiple time points including pre and post-bariatric surgery. In our targeted multiplex screen of 14 selected pancreatic specific circulating transcripts, we identified 13 pancreatic specific transcripts that can be amplified from plasma. Furthermore, when quantifying the amplicons obtained in the short-term post-surgery (2 weeks–1 month) and long-term (3–12 months), we observed a consistent reduction of circulating GCG transcripts during short term post-surgery. Across the cohort, GCG cfmRNA levels correlated significantly with common metrics of improvement following bariatric surgery such as: haemoglobin A1c levels (R: −0.41, p-value: 0.0039) and percentage of excess weight loss (R: 0.29, p-value: 0.046).
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Affiliation(s)
- Kong Kiat Whye
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - E ShyongTai
- Division of Endocrinology, Department of Medicine, National University Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Asim Shabbir
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Surgery, National University Hospital, Singapore, Singapore
| | - Chin Meng Khoo
- Division of Endocrinology, Department of Medicine, National University Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Winston Koh
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
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28
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Assessment of Circulating Nucleic Acids in Cancer: From Current Status to Future Perspectives and Potential Clinical Applications. Cancers (Basel) 2021; 13:cancers13143460. [PMID: 34298675 PMCID: PMC8307284 DOI: 10.3390/cancers13143460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Current approaches for cancer detection and characterization are based on radiological procedures coupled with tissue biopsies, despite relevant limitations in terms of overall accuracy and feasibility, including relevant patients' discomfort. Liquid biopsies enable the minimally invasive collection and analysis of circulating biomarkers released from cancer cells and stroma, representing therefore a promising candidate for the substitution or integration in the current standard of care. Despite the potential, the current clinical applications of liquid biopsies are limited to a few specific purposes. The lack of standardized procedures for the pre-analytical management of body fluids samples and the detection of circulating biomarkers is one of the main factors impacting the effective advancement in the applicability of liquid biopsies to clinical practice. The aim of this work, besides depicting current methods for samples collection, storage, quality check and biomarker extraction, is to review the current techniques aimed at analyzing one of the main circulating biomarkers assessed through liquid biopsy, namely cell-free nucleic acids, with particular regard to circulating tumor DNA (ctDNA). ctDNA current and potential applications are reviewed as well.
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29
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Chalasani N, Toden S, Sninsky JJ, Rava RP, Braun JV, Gawrieh S, Zhuang J, Nerenberg M, Quake SR, Maddala T. Noninvasive stratification of nonalcoholic fatty liver disease by whole transcriptome cell-free mRNA characterization. Am J Physiol Gastrointest Liver Physiol 2021; 320:G439-G449. [PMID: 33501884 PMCID: PMC8238173 DOI: 10.1152/ajpgi.00397.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Hepatic fibrosis stage is the most important determinant of outcomes in patients with nonalcoholic fatty liver disease (NAFLD). There is an urgent need for noninvasive tests that can accurately stage fibrosis and determine efficacy of interventions. Here, we describe a novel cell-free (cf)-mRNA sequencing approach that can accurately and reproducibly profile low levels of circulating mRNAs and evaluate the feasibility of developing a cf-mRNA-based NAFLD fibrosis classifier. Using separate discovery and validation cohorts with biopsy-confirmed NAFLD (n = 176 and 59, respectively) and healthy subjects (n = 23), we performed serum cf-mRNA RNA-Seq profiling. Differential expression analysis identified 2,498 dysregulated genes between patients with NAFLD and healthy subjects and 134 fibrosis-associated genes in patients with NAFLD. Comparison between cf-mRNA and liver tissue transcripts revealed significant overlap of fibrosis-associated genes and pathways indicating that the circulating cf-mRNA transcriptome reflects molecular changes in the livers of patients with NAFLD. In particular, metabolic and immune pathways reflective of known underlying steatosis and inflammation were highly dysregulated in the cf-mRNA profile of patients with advanced fibrosis. Finally, we used an elastic net ordinal logistic model to develop a classifier that predicts clinically significant fibrosis (F2-F4). In an independent cohort, the cf-mRNA classifier was able to identify 50% of patients with at least 90% probability of clinically significant fibrosis. We demonstrate a novel and robust cf-mRNA-based RNA-Seq platform for noninvasive identification of diverse hepatic molecular disruptions and for fibrosis staging with promising potential for clinical trials and clinical practice.NEW & NOTEWORTHY This work is the first study, to our knowledge, to utilize circulating cell-free mRNA sequencing to develop an NAFLD diagnostic classifier.
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Affiliation(s)
- Naga Chalasani
- 1Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | | | | | | | | | - Samer Gawrieh
- 1Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | | | | | - Stephen R. Quake
- 3Departments of Bioengineering and Applied Physics, Stanford University and Chan Zuckerberg Biohub, Stanford, California
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30
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Gowri Sankar S, Alwin Prem Anand A. Cytokine IP-10 and GM-CSF are prognostic biomarkers for severity in secondary dengue infection. Hum Immunol 2021; 82:438-445. [PMID: 33766427 DOI: 10.1016/j.humimm.2021.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/01/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023]
Abstract
Dengue virus (DENV) infection is mostly prevalent in tropical and sub-tropical regions of the world. Though most DENV infections are self-limiting febrile like-illness, a small proportion of secondary infection is fatal, if untreated symptomatically. Among various factors involved in severe dengue, immune enhancement by cytokine is the major one. The objective of the study is to elucidate serum cytokine expression among primary and secondary infection and determine if any signature cytokine is correlated with disease severity. Seventy-six serum samples at acute time points were collected during the 2017 DENV outbreak in Madurai, Tamil Nadu. Among the 76 serum samples, 49 belong to primary and 27 to secondary DENV infection. Interestingly, a large number of primary infection presented with DHF/DSS symptoms and, children were found prone to DHF and DSS in secondary infection. The serum samples were analysed for inflammatory cytokines, namely IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-17A, IFN-γ, TNF-α, IP-10 and GM-CSF using ELISA assay as well as mRNA analysis using qPCR. Among the 12 inflammatory cytokines analysed IP-10 and GMCSF mRNA and protein shows significant upregulation in secondary infection. Similarly, a strong correlation was observed between GM-CSF and IP-10 with thrombocytopenia, ascites, serous effusion and spontaneous bleeding. Based on the observations, GM-CSF and IP-10 could be a potential prognostic biomarkers for secondary DENV infection.
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Affiliation(s)
- S Gowri Sankar
- ICMR-Vector Control Research Center - Field Station, Madurai 625002, Tamil Nadu, India.
| | - A Alwin Prem Anand
- DBT - BIF Centre (Under DBT BTISNet Scheme), Lady Doak College, Madurai 625002, Tamil Nadu, India
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Espinosa C, Becker M, Marić I, Wong RJ, Shaw GM, Gaudilliere B, Aghaeepour N, Stevenson DK. Data-Driven Modeling of Pregnancy-Related Complications. Trends Mol Med 2021; 27:762-776. [PMID: 33573911 DOI: 10.1016/j.molmed.2021.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/01/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
A healthy pregnancy depends on complex interrelated biological adaptations involving placentation, maternal immune responses, and hormonal homeostasis. Recent advances in high-throughput technologies have provided access to multiomics biological data that, combined with clinical and social data, can provide a deeper understanding of normal and abnormal pregnancies. Integration of these heterogeneous datasets using state-of-the-art machine-learning methods can enable the prediction of short- and long-term health trajectories for a mother and offspring and the development of treatments to prevent or minimize complications. We review advanced machine-learning methods that could: provide deeper biological insights into a pregnancy not yet unveiled by current methodologies; clarify the etiologies and heterogeneity of pathologies that affect a pregnancy; and suggest the best approaches to address disparities in outcomes affecting vulnerable populations.
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Affiliation(s)
- Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
| | - Ivana Marić
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald J Wong
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Gary M Shaw
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA; Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - David K Stevenson
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Lee S, Zhou J, Li KHC, Leung KSK, Lakhani I, Liu T, Wong ICK, Mok NS, Mak C, Jeevaratnam K, Zhang Q, Tse G. Territory-wide cohort study of Brugada syndrome in Hong Kong: predictors of long-term outcomes using random survival forests and non-negative matrix factorisation. Open Heart 2021; 8:e001505. [PMID: 33547222 PMCID: PMC7871343 DOI: 10.1136/openhrt-2020-001505] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Brugada syndrome (BrS) is an ion channelopathy that predisposes affected patients to spontaneous ventricular tachycardia/fibrillation (VT/VF) and sudden cardiac death. The aim of this study is to examine the predictive factors of spontaneous VT/VF. METHODS This was a territory-wide retrospective cohort study of patients diagnosed with BrS between 1997 and 2019. The primary outcome was spontaneous VT/VF. Cox regression was used to identify significant risk predictors. Non-linear interactions between variables (latent patterns) were extracted using non-negative matrix factorisation (NMF) and used as inputs into the random survival forest (RSF) model. RESULTS This study included 516 consecutive BrS patients (mean age of initial presentation=50±16 years, male=92%) with a median follow-up of 86 (IQR: 45-118) months. The cohort was divided into subgroups based on initial disease manifestation: asymptomatic (n=314), syncope (n=159) or VT/VF (n=41). Annualised event rates per person-year were 1.70%, 0.05% and 0.01% for the VT/VF, syncope and asymptomatic subgroups, respectively. Multivariate Cox regression analysis revealed initial presentation of VT/VF (HR=24.0, 95% CI=1.21 to 479, p=0.037) and SD of P-wave duration (HR=1.07, 95% CI=1.00 to 1.13, p=0.044) were significant predictors. The NMF-RSF showed the best predictive performance compared with RSF and Cox regression models (precision: 0.87 vs 0.83 vs. 0.76, recall: 0.89 vs. 0.85 vs 0.73, F1-score: 0.88 vs 0.84 vs 0.74). CONCLUSIONS Clinical history, electrocardiographic markers and investigation results provide important information for risk stratification. Machine learning techniques using NMF and RSF significantly improves overall risk stratification performance.
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Affiliation(s)
- Sharen Lee
- Cardiovascular Analytics Group, Laboratory of Cardiovascular Physiology, Hong Kong, China
| | - Jiandong Zhou
- School of Data Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Ka Hou Christien Li
- Faculty of Medicine, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | | | - Ishan Lakhani
- Cardiovascular Analytics Group, Laboratory of Cardiovascular Physiology, Hong Kong, China
| | - Tong Liu
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease, Department of Cardiology, Tianjin Institute of Cardiology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Ian Chi Kei Wong
- Research department of Practice and Policy, University College London School of Pharmacy, London, UK
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Ngai Shing Mok
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong, Hong Kong
| | - Chloe Mak
- Department of Pathology, Hong Kong Children's Hospital, Hong Kong, Hong Kong
| | - Kamalan Jeevaratnam
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Qingpeng Zhang
- School of Data Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Gary Tse
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease, Department of Cardiology, Tianjin Institute of Cardiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
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Ethical, Legal and Social Issues (ELSI) Associated with Non-Invasive Prenatal Testing: Reflections on the Evolution of Prenatal Diagnosis and Procreative Choices. Genes (Basel) 2021; 12:genes12020204. [PMID: 33573312 PMCID: PMC7911180 DOI: 10.3390/genes12020204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
New technologies such as non-invasive prenatal testing (NIPT), capable of analyzing cell-free fetal DNA in the maternal bloodstream, have become increasingly widespread and available, which has in turn led to ethical and policy challenges that need addressing. NIPT is not yet a diagnostic tool, but can still provide information about fetal genetic characteristics (including sex) very early in pregnancy, and there is no denying that it offers valuable opportunities for pregnant women, particularly those at high risk of having a child with severe genetic disorders or seeking an alternative to invasive prenatal testing. Nonetheless, the ethical, legal and social implications (ELSI) include multiple aspects of informed decision-making, which can entail risks for the individual right to procreative autonomy, in addition to the potential threats posed by sex-selective termination of pregnancy (in light of the information about fetal sex within the first trimester), and the stigmatization and discrimination of disabled individuals. After taking such daunting challenges into account and addressing NIPT-related medicolegal complexities, the review's authors highlight the need for an ethically and legally sustainable framework for the implementation of NIPT, which seems poised to become a diagnostic tool, as its scope is likely to broaden in the near future.
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Moufarrej MN, Wong RJ, Shaw GM, Stevenson DK, Quake SR. Investigating Pregnancy and Its Complications Using Circulating Cell-Free RNA in Women's Blood During Gestation. Front Pediatr 2020; 8:605219. [PMID: 33381480 PMCID: PMC7767905 DOI: 10.3389/fped.2020.605219] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
In recent years, there have been major advances in the application of non-invasive techniques to predict pregnancy-related complications, for example by measuring cell-free RNA (cfRNA) in maternal blood. In contrast to cell-free DNA (cfDNA), which is already in clinical use to diagnose fetal aneuploidy, circulating RNA levels can correspond with tissue-specific gene expression and provide a snapshot of prenatal health across gestation. Here, we review the physiologic origins of cfRNA and its novel applications and corresponding challenges to monitor fetal and maternal health and predict pregnancy-related complications.
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Affiliation(s)
- Mira N Moufarrej
- Departments of Bioengineering and Applied Physics, Stanford University, and Chan Zuckerberg Biohub, Stanford, CA, United States
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, and Chan Zuckerberg Biohub, Stanford, CA, United States
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