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Cowan AD, Rasmussen M, Jain M, Tribe RM. Predicting Preterm Birth Using Cell-Free Ribonucleic Acid. Clin Perinatol 2024; 51:379-389. [PMID: 38705647 DOI: 10.1016/j.clp.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Spontaneous preterm birth (sPTB) is a complex and clinically heterogeneous condition that remains incompletely understood, leading to insufficient interventions to effectively prevent it from occurring. Cell-free ribonucleic acid signatures in the maternal circulation have the potential to identify biologically relevant subtypes of sPTB. These could one day be used to predict and prevent sPTB in asymptomatic individuals, and to aid in prognosis and management for individuals presenting with threatened preterm labor and preterm prelabor rupture of membranes.
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Affiliation(s)
- Alison D Cowan
- Department of Medical Affairs, Mirvie, Inc., 651 Gateway Boulevard, Suite 1200, South San Francisco, CA 94080, USA.
| | - Morten Rasmussen
- Department of Research and Development, Mirvie, Inc., 651 Gateway Boulevard, Suite 1200, South San Francisco, CA 94080, USA
| | - Maneesh Jain
- Mirvie, Inc., 651 Gateway Boulevard, Suite 1200, South San Francisco, CA 94080, USA
| | - Rachel M Tribe
- Department of Women and Children's Health, School of Life Course and Population Sciences, King's College London, St. Thomas's Hospital Campus, Westminster Bridge Road, London SE1 7EH, UK
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2
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Liu HE, Vuppalapaty M, Hoerner CR, Bergstrom CP, Chiu M, Lemaire C, Che J, Kaur A, Dimmick A, Liu S, Metzner TJ, Araya M, Crouse S, Sprenger-Haussels M, Schlumpberger M, Leppert JT, Hauch S, Sollier E, Fan AC. Detecting androgen receptor (AR), AR variant 7 (AR-V7), prostate-specific membrane antigen (PSMA), and prostate-specific antigen (PSA) gene expression in CTCs and plasma exosome-derived cfRNA in patients with metastatic castration-resistant prostate cancer (mCRPC) by integrating the VTX-1 CTC isolation system with the QIAGEN AdnaTest. BMC Cancer 2024; 24:482. [PMID: 38627648 PMCID: PMC11022466 DOI: 10.1186/s12885-024-12139-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Therapies for metastatic castration-resistant prostate cancer (mCRPC) include targeting the androgen receptor (AR) with androgen receptor inhibitors (ARIs) and prostate-specific membrane antigen (PSMA). Having the ability to detect AR, AR splice variant 7 (AR-V7), or PSMA in circulating tumor cells (CTCs) or circulating exosomal cell-free RNA (cfRNA) could be helpful to guide selection of the appropriate therapy for each individual patient. The Vortex Biosciences VTX-1 system is a label-free CTC isolation system that enables the detection of the expression of multiple genes in both CTCs and exosomal cfRNA from the same blood sample in patients with mCRPC. Detection of both AR-V7 and PSMA gene expression in both CTCs and cfRNA simultaneously has not yet been reported. METHODS To characterize the combined VTX-1-AdnaDetect workflow, 22Rv1 cancer cells were spiked into blood from healthy donors and processed with the VTX-1 to mimic patient samples and assess performances (capture efficiency, purity, AR and AR-V7 expression). Then, we collected 19 blood samples from 16 patients with mCRPC and therapeutic resistance to androgen receptor inhibitors (ARIs). Plasma was separated and the plasma-depleted blood was processed further with the VTX-1 to collect CTCs. Both plasma exosomal cfRNA and CTCs were subsequently analyzed for AR, AR-V7, PSMA, and prostate-specific antigen (PSA) mRNA expression using the AdnaTest ProstateCancerPanel AR-V7 assay. RESULTS AR-V7 expression could be detected in 22Rv1 cells spiked into blood from healthy volunteers as well as in CTCs and plasma-derived exosomal cfRNA from patients with mCRPC by processing blood with the VTX-1 CTC isolation system followed by the AdnaTest ProstateCancerPanel AR-V7 assay. 94.7% of patient blood samples (18/19) had detectable AR expression in either CTCs or exosomal cfRNA (16 in CTCs, 12 in cfRNA). 15.8% of the 19 patient blood samples (3/19) were found to have AR-V7-positive (AR-V7+) CTCs, one of which was also AR-V7+ in the exosomal cfRNA analysis. 42.1% of patient blood samples (8/19) were found to be PSMA positive (PSMA+): 26.3% (5/19) were PSMA+ in the CTC analysis and 31.6% (6/19) were PSMA+ in the exosomal cfRNA analysis. Of those 8 PSMA+ samples, 2 had detectable PSMA only in CTCs, and 3 had detectable PSMA only in exosomal cfRNA. CONCLUSION VTX-1 enables isolation of CTCs and plasma exosomes from a single blood draw and can be used for detecting AR-V7 and PSMA mRNA in both CTCs and cfRNA in patients with mCRPC and resistance to ARIs. This technology facilitates combining RNA measurements in CTCs and exosomal cfRNA for future studies to develop potentially clinically relevant cancer biomarker detection in blood.
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Affiliation(s)
| | | | - Christian R Hoerner
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Colin P Bergstrom
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Comprehensive Cancer Center, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - James Che
- Vortex Biosciences, Inc, Pleasanton, CA, USA
| | | | | | - Sean Liu
- Vortex Biosciences, Inc, Pleasanton, CA, USA
| | - Thomas J Metzner
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Comprehensive Cancer Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Menna Araya
- Stanford Comprehensive Cancer Center, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | - John T Leppert
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Comprehensive Cancer Center, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Alice C Fan
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Comprehensive Cancer Center, Stanford University School of Medicine, Stanford, CA, USA.
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Moufarrej MN, Winn VD, Quake SR. Cell-Free Nucleic Acids for Early Prediction of Preeclampsia. Curr Hypertens Rep 2024; 26:175-182. [PMID: 38147201 DOI: 10.1007/s11906-023-01291-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2023] [Indexed: 12/27/2023]
Abstract
PURPOSE OF REVIEW This review summarizes the potential of cell-free nucleic acids for predicting preeclampsia, contrasts them with other methods, and discusses these findings' relevance to preeclampsia's pathogenesis and care. RECENT FINDINGS Recent studies have demonstrated the utility of cell-free nucleic acids in early preeclampsia risk prediction. Encouragingly, nucleic acid measurement exhibits similar or better sensitivity as compared to standard screening assays and furthermore sheds light on preeclampsia's underlying placental biology. Over the past decade, liquid biopsies measuring cell-free nucleic acids have found diverse applications, including in prenatal care. Recent advances have extended their utility to predict preeclampsia, a major cause of maternal mortality. These assays assess methylation patterns in cell-free DNA (cfDNA) or gene levels in cell-free RNA (cfRNA). Currently, preeclampsia care focuses on blood pressure control, seizure prevention, and delivery. If validated, early prediction of preeclampsia through liquid biopsies can improve maternal health and deepen our understanding of its causes.
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Affiliation(s)
| | | | - Stephen R Quake
- Department of Bioengineering and Applied Physics, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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4
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Shi H, Ge Q, Pan M, Sheng Y, Qi T, Zhou Y, Sun Y, Bai Y, Cai L. Agarose amplification based sequencing characterization cell-free RNA in preimplantation spent embryo medium. Anal Chim Acta 2024; 1296:342331. [PMID: 38401939 DOI: 10.1016/j.aca.2024.342331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND The cell-free RNA (cf-RNA) of spent embryo medium (SEM) has aroused a concern of academic and clinical researchers for its potential use in non-invasive embryo screening. However, comprehensive characterization of cf-RNA from SEM still presents significant technical challenges, primarily due to the limited volume of SEM. Hence, there is urgently need to a small input liquid volume and ultralow amount of cf-RNA library preparation method to unbiased cf-RNA sequencing from SEM. (75) RESULT: Here, we report a high sensitivity agarose amplification-based cf-RNA sequencing method (SEM-Acf) for human preimplantation SEM cf-RNA analysis. It is a cf-RNA sequencing library preparation method by adding agarose amplification. The agarose amplification sensitivity (0.005 pg) and efficiency (105.35 %) were increased than that of without agarose addition (0.45 pg and 96.06 %) by ∼ 90 fold and 9.29 %, respectively. Compared with SMART sequencing (SMART-seq), the correlation of gene expression was stronger in different SEM samples by using SEM-Acf. The cf-RNA number of detected and coverage uniformity of 3' end were significantly increased. The proportion of 5' end adenine, alternative splicing events and short fragments (<400 bp) were increased. It is also found that 4-mer end motifs of cf-RNA fragments was significantly differences between different embryonic stage by day3 spent cleavage medium and day5/6 spent blastocyst medium. (141) SIGNIFICANCE: This study established an efficient SEM amplification and library preparation method. Additionally, we successfully described the characterizations of SEM cf-RNA in preimplantation embryo using SEM-Acf, including expression features and fragment lengths. SEM-Acf facilitates the exploration of cf-RNA as a noninvasive embryo screening biomarker, and opens up potential clinical utilities of small input liquid volume and ultralow amount cf-RNA sequencing. (59).
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Affiliation(s)
- Huajuan Shi
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Min Pan
- School of Medicine, Southeast University, Nanjing, 210097, China
| | - Yuqi Sheng
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ting Qi
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ying Zhou
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yuqing Sun
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Lingbo Cai
- Clinical Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China.
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Jalaleddine N, Gaudet M, Mogas A, Hachim M, Senok A, Saheb Sharif-Askari N, Mahboub B, Halwani R, Hamid Q, Al Heialy S. Cell free ACE2 RNA: A potential biomarker of COVID-19 severity. Respir Med 2023; 219:107409. [PMID: 37729955 DOI: 10.1016/j.rmed.2023.107409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/29/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023]
Abstract
Despite the downward trend of COVID-19 pandemic and increased immunity of the general population, COVID-19 is still an elusive disease with risks due to emerging variants. Fast and reliable diagnosis of COVID-19 disease would allow better therapeutic interventions for patients at risk to develop more severe outcomes. Cell-free RNAs (cfRNAs) have been proven to be an effective biomarker in cancer and infectious diseases. It has been reported that cfRNAs are amplified in the bloodstream of these patients and at earlier stages of the disease, reflecting tissue damage. Hence, we hypothesize that cfRNAs may serve as a potential indicator of COVID-19 disease severity. To our knowledge, this is the first report to display a significant link between COVID-19 severity and cfRNA of angiotensin converting enzyme-2 (ACE2), the receptor for SARS-CoV-2 virus. qRT-PCR analysis of liquid biopsies from COVID-19 patients (n = 82) displayed a significant increase in ACE2-cfRNA levels in patients with severe manifestations. This finding correlated with blood biomarkers (ANC, WBC, and Creatinine) that were also significantly increased in these patients. We previously showed that bronchial cells from obese subjects express higher ACE2 levels, hence, we further analysed the involvement of obesity as a main contributor to severe outcomes. We confirm a significant increase of ACE2-cfRNA in the plasma of obese/overweight (Ob/Ov) COVID-19 patients compared to lean subjects, with no observed significant change in blood biomarkers. These findings suggest that monitoring ACE2-cfRNAs, as a biomarker, during COVID-19 infection may allow for better disease management, specifically for severe-COVID-19 patients.
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Affiliation(s)
- Nour Jalaleddine
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mellissa Gaudet
- Meakins-Christie Laboratories, Research Institute of the McGill University Healthy Center, Montreal, Quebec, Canada
| | - Andrea Mogas
- Meakins-Christie Laboratories, Research Institute of the McGill University Healthy Center, Montreal, Quebec, Canada
| | - Mahmood Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Bassam Mahboub
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; Department of Pulmonary Medicine and Allergy and Sleep Medicine, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Rabih Halwani
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; Prince Abdullah Ben Khaled Celiac Disease Research Chair, Department of Paediatrics, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Qutayba Hamid
- Meakins-Christie Laboratories, Research Institute of the McGill University Healthy Center, Montreal, Quebec, Canada; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates; Meakins-Christie Laboratories, Research Institute of the McGill University Healthy Center, Montreal, Quebec, Canada.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Garofalo M, Bonanno S, Marcuzzo S, Pandini C, Scarian E, Dragoni F, Di Gerlando R, Bordoni M, Parravicini S, Gellera C, Masson R, Dosi C, Zanin R, Pansarasa O, Cereda C, Berardinelli A, Gagliardi S. Preliminary insights into RNA in CSF of pediatric SMA patients after 6 months of nusinersen. Biol Direct 2023; 18:57. [PMID: 37705059 PMCID: PMC10498611 DOI: 10.1186/s13062-023-00413-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a rare autosomal-recessive neurodegenerative disorder caused by mutations in survival motor neuron 1 (SMN1) gene, and consequent loss of function of SMN protein, which results in progressive loss of lower motor neurons, and muscular wasting. Antisense oligonucleotide (ASO) nusinersen (Spinraza®) modulates the pre-mRNA splicing of the SMN2 gene, allowing rebalance of biologically active SMN. It is administered intrathecally via lumbar puncture after removing an equal amount of cerebrospinal fluid (CSF). Its effect was proven beneficial and approved since 2017 for SMA treatment. Given the direct effect of nusinersen on RNA metabolism, the aim of this project was to evaluate cell-free RNA (cfRNA) in CSF of SMA patients under ASOs treatment for biomarker discovery. METHODS By RNA-sequencing approach, RNA obtained from CSF of pediatric SMA type 2 and 3 patients was processed after 6 months of nusinersen treatment, at fifth intrathecal injection (T6), and compared to baseline (T0). RESULTS We observed the deregulation of cfRNAs in patients at T6 and we were able to classify these RNAs into disease specific, treatment specific and treatment dependent. Moreover, we subdivided patients into "homogeneous" and "heterogeneous" according to their gene expression pattern. The "heterogeneous" group showed peculiar activation of genes coding for ribosomal components, meaning that in these patients a different molecular effect of nusinersen is observable, even if this specific molecular response was not referable to a clinical pattern. CONCLUSIONS This study provides preliminary insights into modulation of gene expression dependent on nusinersen treatment and lays the foundation for biomarkers discovery.
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Affiliation(s)
| | - S Bonanno
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - S Marcuzzo
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - C Pandini
- Department of Biosciences, University of Milan, Milan, Italy
| | - E Scarian
- IRCCS Mondino Foundation, Pavia, Italy
| | - F Dragoni
- IRCCS Mondino Foundation, Pavia, Italy
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - R Di Gerlando
- IRCCS Mondino Foundation, Pavia, Italy
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - M Bordoni
- IRCCS Mondino Foundation, Pavia, Italy
| | - S Parravicini
- IRCCS Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - C Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - R Masson
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - C Dosi
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - R Zanin
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | | | - C Cereda
- Center of Functional Genomics and Rare Diseases, V. Buzzi Children's Hospital, 20154, Milan, Italy
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Mullins KE, Seneviratne C, Shetty AC, Jiang F, Christenson R, Stass S. Proof of concept: Detection of cell free RNA from EDTA plasma in patients with lung cancer and non-cancer patients. Clin Biochem 2023; 118:110583. [PMID: 37182637 DOI: 10.1016/j.clinbiochem.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/16/2023]
Abstract
INTRODUCTION Nucleic acid sequencing technologies have advanced significantly in recent years, thereby allowing for the development of liquid biopsies as new means to detect cancer biomarkers and cancer heterogenicity. Most of the assays available, clinically, focus on cell free DNA (cfDNA), however, cell free RNA (cfRNA) is also present. cfRNA has the potential to complement and improve cancer detection especially in cancers like lung cancer, which are usually only diagnosed at late stages and therefore have poor long-term survival outcomes. METHODS Remnant EDTA plasma was collected from lung cancer patients and non-cancer individuals at the University of Maryland Medical Center. RNA was extracted and processed for next generation sequencing with a tagmentation-based library preparation approach. RESULTS cfRNA was successfully extracted and sequenced from 52 EDTA-treated plasma samples with volumes as low as 1.5 mL. This quantity was sufficient to prepare libraries with the length of libraries averaging from 264 bp to 381 bp and resulted in over 2.2 to 3.6 million total sequence reads respectively. Sequential dilution of cfRNA samples from healthy individuals indicated that the starting cfRNA concentration influenced the detection of differentially expressed genes. CONCLUSIONS This proof-of-concept study provides a framework for screening cfRNA for identifying biomarkers for early detection of lung cancer (and other cancers), using minimal amounts of samples (1.5 mL) from standard EDTA 3-mL collection tubes routinely used for patient care. Further studies in large populations are required to establish limit of detection and other parameters including precision, accuracy, sensitivity, and specificity, to standardize this method.
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Affiliation(s)
- Kristin E Mullins
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA; Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD, USA.
| | - Chamindi Seneviratne
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA; The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amol C Shetty
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Feng Jiang
- Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD, USA
| | - Robert Christenson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA; Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD, USA
| | - Sanford Stass
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA; Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD, USA
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Albitar M, Zhang H, Charifa A, Ip A, Ma W, McCloskey J, Donato M, Siegel D, Waintraub S, Gutierrez M, Pecora A, Goy A. Combining cell-free RNA with cell-free DNA in liquid biopsy for hematologic and solid tumors. Heliyon 2023; 9:e16261. [PMID: 37251903 PMCID: PMC10208940 DOI: 10.1016/j.heliyon.2023.e16261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
Current use of liquid biopsy is based on cell-free DNA (cfDNA) and the evaluation of mutations or methylation pattern. However, expressed RNA can capture mutations, changes in expression levels due to methylation, and provide information on cell of origin, growth, and proliferation status. We developed an approach to isolate cell-free total nucleic acid (cfDNA) and used targeted next generation sequencing to sequence cell-free RNA (cfRNA) and cfDNA as new approach in liquid biopsy. We demonstrate that cfRNA is overall more sensitive than cfDNA in detecting mutations. We show that cfRNA is reliable in detecting fusion genes and cfDNA is reliable in detecting chromosomal gains and losses. cfRNA levels of various solid tumor biomarkers were significantly higher (P < 0.0001) in samples from solid tumors as compared with normal control. Similarly, cfRNA lymphoid markers and cfRNA myeloid markers were all higher in lymphoid and myeloid neoplasms, respectively as compared with control (P < 0.0001). Using machine learning we demonstrate cfRNA was highly predictive of diagnosis (AUC >0.98) of solid tumors, B-cell lymphoid neoplasms, T-cell lymphoid neoplasms, and myeloid neoplasms. In evaluating the host immune system, cfRNA CD4:CD8B and CD3D:CD19 ratios in normal controls were as expected (median: 5.92 and 6.87, respectively) and were significantly lower in solid tumors (P < 0.0002). This data suggests that liquid biopsy combining analysis of cfRNA with cfDNA is practical and may provide helpful information in predicting genomic abnormalities, diagnosis of neoplasms and evaluating both the tumor biology and the host response.
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Affiliation(s)
- Maher Albitar
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Hong Zhang
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Ahmad Charifa
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Andrew Ip
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Wanlong Ma
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - James McCloskey
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Michele Donato
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - David Siegel
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Stanley Waintraub
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Martin Gutierrez
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Andrew Pecora
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Andre Goy
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
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Verebi C, Nectoux J, Gorwood P, Le Strat Y, Duriez P, Ramoz N, Bienvenu T. A systematic literature review and meta-analysis of circulating nucleic acids as biomarkers in psychiatry. Prog Neuropsychopharmacol Biol Psychiatry 2023; 125:110770. [PMID: 37068545 DOI: 10.1016/j.pnpbp.2023.110770] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/14/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
Common mental disorders (CMDs) such as depression, anxiety and post-traumatic stress disorders account for 40% of the global burden of disease. In most psychiatric disorders, both diagnosis and monitoring can be challenging, frequently requiring long-term investigation and follow-up. The discovery of better methods to facilitate accurate and fast diagnosis and monitoring of psychiatric disorders is therefore crucial. Circulating nucleic acids (CNAs) are among these new tools. CNAs (DNA or RNA) can be found circulating in body biofluids, and can be isolated from biological samples such as plasma. They can serve as biomarkers for diagnosis and prognoses. They appear to be promising for disorders (such as psychiatric disorders) that involve organs or structures that are difficult to assess. This review presents an accurate assessment of the current literature about the use of plasma and serum cell-free DNA (cfDNA) as biomarkers for several aspects of psychiatric disorders: diagnosis, prognosis, treatment response, and monitor disease progression. For each psychiatric disorder, we examine the effect sizes to give insights on the efficacy of CNAs as biomarkers. The global effect size for plasma nuclear and mitochondrial cfDNA studies was generally moderate for psychiatric disorders. In addition, we discuss future applications of CNAs and particularly cfDNA as non-invasive biomarkers for these diseases.
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Affiliation(s)
- Camille Verebi
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France; INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France
| | - Juliette Nectoux
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France
| | - Philip Gorwood
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France; Université Paris Cité, GHU Paris Psychiatrie et Neurosciences (CMME), Paris, France
| | - Yann Le Strat
- AP-HP, Department of Psychiatry, Louis Mourier Hospital, Université Paris Cité, Faculté de Médecine, Colombes, France
| | - Philibert Duriez
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France; Université Paris Cité, GHU Paris Psychiatrie et Neurosciences (CMME), Paris, France
| | - Nicolas Ramoz
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France
| | - Thierry Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France; INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France.
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11
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Jin H, Zhang Y, Fan Z, Wang X, Rui C, Xing S, Dong H, Wang Q, Tao F, Zhu Y. Identification of novel cell-free RNAs in maternal plasma as preterm biomarkers in combination with placental RNA profiles. J Transl Med 2023; 21:256. [PMID: 37046301 PMCID: PMC10100253 DOI: 10.1186/s12967-023-04083-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/25/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Preterm birth (PTB) is the main driver of newborn deaths. The identification of pregnancies at risk of PTB remains challenging, as the incomplete understanding of molecular mechanisms associated with PTB. Although several transcriptome studies have been done on the placenta and plasma from PTB women, a comprehensive description of the RNA profiles from plasma and placenta associated with PTB remains lacking. METHODS Candidate markers with consistent trends in the placenta and plasma were identified by implementing differential expression analysis using placental tissue and maternal plasma RNA-seq datasets, and then validated by RT-qPCR in an independent cohort. In combination with bioinformatics analysis tools, we set up two protein-protein interaction networks of the significant PTB-related modules. The support vector machine (SVM) model was used to verify the prediction potential of cell free RNAs (cfRNAs) in plasma for PTB and late PTB. RESULTS We identified 15 genes with consistent regulatory trends in placenta and plasma of PTB while the full term birth (FTB) acts as a control. Subsequently, we verified seven cfRNAs in an independent cohort by RT-qPCR in maternal plasma. The cfRNA ARHGEF28 showed consistence in the experimental validation and performed excellently in prediction of PTB in the model. The AUC achieved 0.990 for whole PTB and 0.986 for late PTB. CONCLUSIONS In a comparison of PTB versus FTB, the combined investigation of placental and plasma RNA profiles has shown a further understanding of the mechanism of PTB. Then, the cfRNA identified has the capacity of predicting whole PTB and late PTB.
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Affiliation(s)
- Heyue Jin
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, No 81 Meishan Road, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China
| | - Yimin Zhang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, No 81 Meishan Road, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China
| | - Zhigang Fan
- Department of Neonatology, Ma'anshan Maternal and Child Health Hospital, Ma'anshan, Anhui, China
| | - Xianyan Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei, Anhui, China
| | - Chen Rui
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei, Anhui, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongmei Dong
- Department of Obstetrics, Ma'anshan Maternal and Child Health Hospital, Ma'anshan, Anhui, China
| | - Qunan Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, Anhui, China.
- Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Hefei, Anhui, China.
| | - Fangbiao Tao
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China.
- MOE Key Laboratory of Population Health Across Life Cycle, No 81 Meishan Road, Hefei, Anhui, China.
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China.
| | - Yumin Zhu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China.
- MOE Key Laboratory of Population Health Across Life Cycle, No 81 Meishan Road, Hefei, Anhui, China.
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China.
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12
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Li S, Xin K, Pan S, Wang Y, Zheng J, Li Z, Liu X, Liu B, Xu Z, Chen X. Blood-based liquid biopsy: insights into early detection, prediction, and treatment monitoring of bladder cancer. Cell Mol Biol Lett 2023; 28:28. [PMID: 37016296 PMCID: PMC10074703 DOI: 10.1186/s11658-023-00442-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Bladder cancer (BC) is a clinical challenge worldwide with late clinical presentation, poor prognosis, and low survival rates. Traditional cystoscopy and tissue biopsy are routine methods for the diagnosis, prognosis, and monitoring of BC. However, due to the heterogeneity and limitations of tumors, such as aggressiveness, high cost, and limited applicability of longitudinal surveillance, the identification of tumor markers has attracted significant attention in BC. Over the past decade, liquid biopsies (e.g., blood) have proven to be highly efficient methods for the discovery of BC biomarkers. This noninvasive sampling method is used to analyze unique tumor components released into the peripheral circulation and allows serial sampling and longitudinal monitoring of tumor progression. Several liquid biopsy biomarkers are being extensively studied and have shown promising results in clinical applications of BC, including early detection, detection of microscopic residual disease, prediction of recurrence, and response to therapy. Therefore, in this review, we aim to provide an update on various novel blood-based liquid biopsy markers and review the advantages and current limitations of liquid biopsy in BC therapy. The role of blood-based circulating tumor cells, circulating tumor DNA, cell-free RNA, exosomes, metabolomics, and proteomics in diagnosis, prognosis, and treatment monitoring, and their applicability to the personalized management of BC, are highlighted.
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Affiliation(s)
- Shijie Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Kerong Xin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Shen Pan
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Yang Wang
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, Liaoning, People's Republic of China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Xuefeng Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Bitian Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
| | - Zhenqun Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Shi H, Pan M, Jia E, Lu W, Zhou Y, Sheng Y, Zhao X, Cai L, Ge Q. A comprehensive characterization of cell-free RNA in spent blastocyst medium and quality prediction for blastocyst. Clin Sci (Lond) 2023; 137:129-0. [PMID: 36597876 DOI: 10.1042/cs20220495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/16/2022] [Accepted: 01/03/2023] [Indexed: 01/05/2023]
Abstract
The rate of pregnancy can be affected by many factors in assisted reproductive technology (ART), and one of which is the quality of embryos. Therefore, selecting the embryos with high potential is crucial for the outcome. Fifteen spent blastocyst medium (SBM) samples were collected from 14 patients who received in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI), seven from high-grade embryos and eight from low-grade embryos. Cell-free RNA (cf-RNA) profile of SBM samples were analyzed by RNA sequencing in the present study. It was found that a large amount of cf-RNA were released into SBM, including protein-coding genes (68.9%) and long noncoding RNAs (lncRNAs) (17.26%). Furthermore, a high correlation was observed between blastocyst genes and SBM genes. And the cf-mRNAs of SBM were highly fragmented, and coding sequence (CDS) and untranslated (UTR) regions were released equally. Two hundred and thirty-two differentially expressed genes were identified in high-grade SBM (hSBM) and low-grade SBM (lSBM), which could be potential biomarker in distinguishing the embryos with different quality as an alternative or supplementary approach for subjective morphology criteria. Hence, cf-RNAs sequencing revealed the characterization of circulating transcriptomes of embryos with different quality. Based on the results, the genes related to blastocyst quality were screened, including the genes closely related to translation, immune-signaling pathway, and amino acid metabolism. Overall, the present study showed the types of SBM cf-RNAs, and the integrated analysis of cf-RNAs profiling with morphology grading displayed its potential in predicting blastocyst quality. The present study provided valuable scientific basis for noninvasive embryo selection in ART by RNA-profiling analysis.
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Affiliation(s)
- Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing 210097, China
| | - Erteng Jia
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Wenxiang Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Ying Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Yuqi Sheng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Lingbo Cai
- Clinical Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
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Deleu J, Schoofs K, Decock A, Verniers K, Roelandt S, Denolf A, Verreth J, De Wilde B, Van Maerken T, De Preter K, Vandesompele J. Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA. Hum Genomics 2022; 16:73. [PMID: 36587211 PMCID: PMC9805675 DOI: 10.1186/s40246-022-00446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/19/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Blood plasma, one of the most studied liquid biopsies, contains various molecules that have biomarker potential for cancer detection, including cell-free DNA (cfDNA) and cell-free RNA (cfRNA). As the vast majority of cell-free nucleic acids in circulation are non-cancerous, a laboratory workflow with a high detection sensitivity of tumor-derived nucleic acids is a prerequisite for precision oncology. One way to meet this requirement is by the combined analysis of cfDNA and cfRNA from the same liquid biopsy sample. So far, no study has systematically compared the performance of cfDNA and cfRNA co-purification to increase sensitivity. RESULTS First, we set up a framework using digital PCR (dPCR) technology to quantify cfDNA and cfRNA from human blood plasma in order to compare cfDNA/cfRNA co-purification kit performance. To that end, we optimized two dPCR duplex assays, designed to quantify both cfDNA and cfRNA with the same assays, by ensuring that primers and probes are located within a highly abundant exon. Next, we applied our optimized workflow to evaluate the co-purification performance of two manual and two semi-automated methods over a range of plasma input volumes (0.06-4 mL). Some kits result in higher nucleic acid concentrations in the eluate, while consuming only half of the plasma volume. The combined nucleic acid quantification systematically results in higher nucleic acid concentrations as compared to a parallel quantification of cfDNA and cfRNA in the eluate. CONCLUSIONS We provide a framework to evaluate the performance of cfDNA/cfRNA co-purification kits and have tested two manual and two semi-automated co-purification kits in function of the available plasma input amount and the intended use of the nucleic acid eluate. We demonstrate that the combined quantification of cfDNA and cfRNA has a benefit compared to separate quantification. We foresee that the results of this study are instrumental for clinical applications to help increase mutation detection sensitivity, allowing improved disease detection and monitoring.
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Affiliation(s)
- Jill Deleu
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kathleen Schoofs
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.510942.bTranslational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Anneleen Decock
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kimberly Verniers
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sofie Roelandt
- grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.510942.bTranslational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Angie Denolf
- grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.510942.bTranslational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Joke Verreth
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bram De Wilde
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.410566.00000 0004 0626 3303Department of Paediatric Haematology Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Tom Van Maerken
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.420028.c0000 0004 0626 4023Department of Laboratory Medicine, AZ Groeninge, Kortrijk, Belgium
| | - Katleen De Preter
- grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.510942.bTranslational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Jo Vandesompele
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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税 丽, 许 文, 何 国. [Latest Research Findings on Prediction of Preeclampsia in Pregnant Women Based on Analysis of Cell-Free RNA in Peripheral Blood]. Sichuan Da Xue Xue Bao Yi Xue Ban 2022; 53:1016-1020. [PMID: 36443045 PMCID: PMC10408976 DOI: 10.12182/20220860104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 06/16/2023]
Abstract
Preeclampsia gravely threatens the health of mothers and infants. At present, treatment based on the relevant mechanisms of pathogenesis is still not available, and there is no independent reliable clinical index for early prediction of preeclampsia. According to recent studies, analysis of the cell-free RNA in the peripheral blood of pregnant women has shown that testing certain cell-free RNA levels can help predict in advance the occurrence of preeclampsia before clinical symptoms appear. In this paper, we described the status of research and progress in using maternal cell-free RNA analysis in predicting preeclampsia. In addition, we stated that cell-free RNA in peripheral blood may become a promising, real-time and non-invasive monitoring method that can be used to explore the mechanisms of pathogenesis and pathophysiology of preeclampsia and to identify different subtypes of preeclampsia.
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Affiliation(s)
- 丽萍 税
- 四川大学华西第二医院 产科 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - 文明 许
- 四川大学华西第二医院 产科 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, Sichuan University, Chengdu 610041, China
| | - 国琳 何
- 四川大学华西第二医院 产科 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, Sichuan University, Chengdu 610041, China
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Cabús L, Lagarde J, Curado J, Lizano E, Pérez-Boza J. Current challenges and best practices for cell-free long RNA biomarker discovery. Biomark Res 2022; 10:62. [PMID: 35978416 DOI: 10.1186/s40364-022-00409-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Hulstaert E, Levanon K, Morlion A, Van Aelst S, Christidis AA, Zamar R, Anckaert J, Verniers K, Bahar-Shany K, Sapoznik S, Vandesompele J, Mestdagh P. RNA biomarkers from proximal liquid biopsy for diagnosis of ovarian cancer. Neoplasia 2022; 24:155-164. [PMID: 34998206 PMCID: PMC8740458 DOI: 10.1016/j.neo.2021.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/20/2021] [Indexed: 10/29/2022]
Abstract
BACKGROUND Most ovarian cancer patients are diagnosed at an advanced stage and have a high mortality rate. Current screening strategies fail to improve prognosis because markers that are sensitive for early stage disease are lacking. This medical need justifies the search for novel approaches using utero-tubal lavage as a proximal liquid biopsy. METHODS In this study, we explore the extracellular transcriptome of utero-tubal lavage fluid obtained from 26 ovarian cancer patients and 48 controls using messenger RNA (mRNA) capture and small RNA sequencing. RESULTS We observed an enrichment of ovarian and fallopian tube specific messenger RNAs in utero-tubal lavage fluid compared to other human biofluids. Over 300 mRNAs and 41 miRNAs were upregulated in ovarian cancer samples compared with controls. Upregulated genes were enriched for genes involved in cell cycle activation and proliferation, hinting at a tumor-derived signal. CONCLUSION This is a proof-of-principle that mRNA capture sequencing of utero-tubal lavage fluid is technically feasible, and that the extracellular transcriptome of utero-tubal lavage should be further explored in larger cohorts to assess the diagnostic value of the biomarkers identified in this study. IMPACT Proximal liquid biopsy from the gynecologic tract is a promising source for mRNA and miRNA biomarkers for diagnosis of early-stage ovarian cancer.
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Affiliation(s)
- Eva Hulstaert
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium; Department of Dermatology, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Keren Levanon
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Annelien Morlion
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | | | | | - Ruben Zamar
- Department of Statistics, University of British Columbia, Vancouver, Canada
| | - Jasper Anckaert
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Kimberly Verniers
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Keren Bahar-Shany
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Stav Sapoznik
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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19
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Tucker D, Zheng W, Zhang DH, Dong X. Circular RNA and its potential as prostate cancer biomarkers. World J Clin Oncol 2020; 11:563-572. [PMID: 32879844 PMCID: PMC7443832 DOI: 10.5306/wjco.v11.i8.563] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/09/2020] [Accepted: 07/19/2020] [Indexed: 02/06/2023] Open
Abstract
Advancing knowledge of the transcriptome has revealed that circular RNAs (circRNAs) are widely expressed and evolutionarily conserved molecules that may serve relevant biological roles. More interesting is the accumulating evidence which demonstrates the implication of circRNAs in diseases, especially cancers. This revelation has helped to form the rationale for many studies exploring their utility as clinical biomarkers. CircRNAs are highly stable due to their unique structures, exhibit some tissue specificity, and are enriched in exosomes, which facilitate their detection in a range of body fluids. These properties make circRNAs ideal candidates for biomarker development in many diseases. This review will outline the discovery, biogenesis, and proposed functions of circRNAs.
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Affiliation(s)
- Dwayne Tucker
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Wei Zheng
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou 310024, Zhejiang Province, China
| | - Da-Hong Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou 310024, Zhejiang Province, China
| | - Xuesen Dong
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
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20
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Fettke H, Kwan EM, Docanto MM, Bukczynska P, Ng N, Graham LJK, Mahon K, Hauser C, Tan W, Wang XH, Zhao Z, Zheng T, Zhou K, Du P, Yu J, Huang Y, Jia S, Kohli M, Horvath LG, Azad AA. Combined Cell-free DNA and RNA Profiling of the Androgen Receptor: Clinical Utility of a Novel Multianalyte Liquid Biopsy Assay for Metastatic Prostate Cancer. Eur Urol 2020; 78:173-180. [PMID: 32487321 DOI: 10.1016/j.eururo.2020.03.044] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 03/25/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND The androgen receptor (AR) remains a critical driver in metastatic castration-resistant prostate cancer (mCRPC). Profiling AR aberrations in both circulating DNA and RNA may identify key predictive and/or prognostic biomarkers in the context of contemporary systemic therapy. OBJECTIVE To profile AR aberrations in circulating nucleic acids and correlate with clinical outcomes. DESIGN, SETTING, AND PARTICIPANTS We prospectively enrolled 67 mCRPC patients commencing AR pathway inhibitors (ARPIs; n = 41) or taxane chemotherapy (n = 26). Using a first-in-class next-generation sequencing-based assay, we performed integrated cell-free DNA (cfDNA) and cell-free RNA (cfRNA) profiling from a single 10 ml blood tube. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Kaplan-Meier survival estimates and multivariable Cox regression analyses were used to assess associations between clinical outcomes and the following AR aberrations: copy number variation, splice variants (AR-V7 and AR-V9) and somatic mutations. RESULTS AND LIMITATIONS Cell-free DNA and cfRNA were successfully sequenced in 67 (100%) and 59 (88%) patients, respectively. Thirty-six (54%) patients had one or more AR aberrations. AR gain and cumulative number of AR aberrations were independently associated with clinical/radiographic progression-free survival (PFS; hazard ratio [HR] 3.2, p = 0.01 and HR 3.0 for 0 vs ≥2, p = 0.04) and overall survival (HR 2.8, p = 0.04 and HR 2.9 for 0 vs ≥2, p = 0.03). Notably, concurrent AR gain and AR splice variant expression (AR gain/AR-V+) was associated with shorter prostate-specific antigen PFS on both ARPIs (HR 6.7, p = 0.009) and chemotherapy (HR 3.9, p = 0.04). Importantly, key findings were validated in an independent cohort of mCRPC patients (n = 40), including shorter OS in AR gain/AR-V+ disease (HR 3.3, p = 0.02). Limitations include sample size and follow-up period. CONCLUSIONS We demonstrate the utility of a novel, multianalyte liquid biopsy assay capable of simultaneously detecting AR alterations in cfDNA and cfRNA. Concurrent profiling of cfDNA and cfRNA may provide vital insights into disease biology and resistance mechanisms in mCRPC. PATIENT SUMMARY In this study of men with advanced prostate cancer, DNA and RNA abnormalities in the androgen receptor detected in blood were associated with poor outcomes on available drug treatments. This information could be used to better guide treatment of advanced prostate cancer.
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Affiliation(s)
- Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia; Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
| | - Maria M Docanto
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Patricia Bukczynska
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Nicole Ng
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Lisa-Jane K Graham
- Medical Oncology, Chris O'Brien Lifehouse, Sydney, New South Wales, Australia
| | - Kate Mahon
- Medical Oncology, Chris O'Brien Lifehouse, Sydney, New South Wales, Australia; University of Sydney, Sydney, New South Wales, Australia; Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Christine Hauser
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Winston Tan
- Department of Oncology, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | | | - Pan Du
- Predicine Inc., Hayward, CA, USA
| | | | | | | | - Manish Kohli
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Lisa G Horvath
- Medical Oncology, Chris O'Brien Lifehouse, Sydney, New South Wales, Australia; University of Sydney, Sydney, New South Wales, Australia; Garvan Institute of Medical Research, Sydney, New South Wales, Australia; Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Arun A Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia; Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
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21
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Tarca AL, Romero R, Pique-Regi R, Pacora P, Done B, Kacerovsky M, Bhatti G, Jaiman S, Hassan SS, Hsu CD, Gomez-Lopez N. Amniotic fluid cell-free transcriptome: a glimpse into fetal development and placental cellular dynamics during normal pregnancy. BMC Med Genomics 2020; 13:25. [PMID: 32050959 PMCID: PMC7017452 DOI: 10.1186/s12920-020-0690-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Background The amniotic fluid (AF) cell-free transcriptome is modulated by physiologic and pathologic processes during pregnancy. AF gene expression changes with advancing gestation reflect fetal development and organ maturation; yet, defining normal expression and splicing patterns for biomarker discovery in obstetrics requires larger heterogeneous cohorts, evaluation of potential confounding factors, and novel analytical approaches. Methods Women with a normal pregnancy who had an AF sample collected during midtrimester (n = 30) or at term gestation (n = 68) were included. Expression profiling at exon level resolution was performed using Human Transcriptome Arrays. Differential expression was based on moderated t-test adjusted p < 0.05 and fold change > 1.25; for differential splicing, a splicing index > 2 and adjusted p < 0.05 were required. Functional profiling was used to interpret differentially expressed or spliced genes. The expression of tissue-specific and cell-type specific signatures defined by single-cell genomics was quantified and correlated with covariates. In-silico validation studies were performed using publicly available datasets. Results 1) 64,071 genes were detected in AF, with 11% of the coding and 6% of the non-coding genes being differentially expressed between midtrimester and term gestation. Expression changes were highly correlated with those previously reported (R > 0.79, p < 0.001) and featured increased expression of genes specific to the trachea, salivary glands, and lung and decreased expression of genes specific to the cardiac myocytes, uterus, and fetal liver, among others. 2) Single-cell RNA-seq signatures of the cytotrophoblast, Hofbauer cells, erythrocytes, monocytes, T and B cells, among others, showed complex patterns of modulation with gestation (adjusted p < 0.05). 3) In 17% of the genes detected, we found differential splicing with advancing gestation in genes related to brain development processes and immunity pathways, including some that were missed based on differential expression analysis alone. Conclusions This represents the largest AF transcriptomics study in normal pregnancy, reporting for the first time that single-cell genomic signatures can be tracked in the AF and display complex patterns of expression during gestation. We also demonstrate a role for alternative splicing in tissue-identity acquisition, organ development, and immune processes. The results herein may have implications for the development of fetal testing to assess placental function and fetal organ maturity.
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Affiliation(s)
- Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA. .,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA.
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA. .,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA. .,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA. .,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA. .,Detroit Medical Center, Detroit, MI, USA. .,Department of Pathology, Hutzel Women's Hospital, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Roger Pique-Regi
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Percy Pacora
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Bogdan Done
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
| | - Marian Kacerovsky
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - Gaurav Bhatti
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sunil Jaiman
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Pathology, Hutzel Women's Hospital, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sonia S Hassan
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chaur-Dong Hsu
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, 𝐸𝑢𝑛𝑖𝑐𝑒 𝐾𝑒𝑛𝑛𝑒𝑑𝑦 𝑆ℎ𝑟𝑖𝑣𝑒𝑟 National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA. .,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicin, Detroit, MI, USA.
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22
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Beck TN, Boumber YA, Aggarwal C, Pei J, Thrash-Bingham C, Fittipaldi P, Vlasenkova R, Rao C, Borghaei H, Cristofanilli M, Mehra R, Serebriiskii I, Alpaugh RK. Circulating tumor cell and cell-free RNA capture and expression analysis identify platelet-associated genes in metastatic lung cancer. BMC Cancer 2019; 19:603. [PMID: 31215484 PMCID: PMC6582501 DOI: 10.1186/s12885-019-5795-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 06/05/2019] [Indexed: 12/25/2022] Open
Abstract
Background Circulating tumor cells (CTC) and plasma cell-free RNA (cfRNA) can serve as biomarkers for prognosis and treatment response in lung cancer. One barrier to the selected or routine use of CTCs and plasma cfRNA in precision oncology is the limited quantity of both, and CTCs are only seen in metastatic disease. As capture of CTCs and plasma cfRNA presents an opportunity to monitor and assess malignancies without invasive procedures, we compared two methods for CTC capture and identification, and profiled mRNA from CTCs and plasma cfRNA to identify potential tumor-associated biomarkers. Methods Peripheral blood was collected from ten patients with small cell lung cancer (SCLC), ten patients with non-small cell lung cancer (NSCLC) and four healthy volunteers. Two methods were used for CTC capture: the standard epithelial cell adhesion molecule (EpCam) CellSearch kit (unicapture) and EpCAM plus HER2, EGFR and MUC-1 specific combined ferrofluid capture (quadcapture). For the quadcapture, anti-cytokeratin 7 (CK7) was additionally used to assist in CTC identification. NanoString analysis was performed on plasma cfRNA and on mRNA from combined ferrofluid isolated CTCs. Expression data was analyzed using STRING and Reactome. Results Unicapture detected CTCs in 40% of NSCLC and 60% of SCLC; whereas, quadcapture/CK7 identified CTCs in 20% of NSCLC and 80% of SCLC. Bioinformatic analysis of NanoString data identified high expression of a platelet factor 4 (PF4)-related group of transcripts. Conclusions Quadcapture ferrofluid reagent did not significantly improve CTC capture efficacy. NanoString analysis based on CTC and plasma cfRNA data highlighted an intriguing PF-4-centric network in patients with metastatic lung cancer. Electronic supplementary material The online version of this article (10.1186/s12885-019-5795-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tim N Beck
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.,Digestive Disease & Surgery Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Yanis A Boumber
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.,Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.,Kazan Federal University, Kazan, Russian Federation
| | - Charu Aggarwal
- Abramson Cancer Center and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jianming Pei
- Genomics Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | - Patricia Fittipaldi
- Protocol Support Laboratory, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | - Chandra Rao
- Janssen Diagnostics LLC, Valley, Huntingdon, PA, 19006, USA
| | - Hossein Borghaei
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.,Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Massimo Cristofanilli
- Feinberg School of Medicine, Robert H Lurie Comprehensive Cancer Center, Chicago, IL, 60611, USA
| | - Ranee Mehra
- Head and Neck Medical Oncology, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD, 21201, USA
| | - Ilya Serebriiskii
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.,Kazan Federal University, Kazan, Russian Federation
| | - R Katherine Alpaugh
- Protocol Support Laboratory, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA. .,Biostatistics Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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23
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Armstrong D, Wildman DE. Extracellular Vesicles and the Promise of Continuous Liquid Biopsies. J Pathol Transl Med 2018; 52:1-8. [PMID: 29370511 PMCID: PMC5784223 DOI: 10.4132/jptm.2017.05.21] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/13/2017] [Accepted: 05/21/2017] [Indexed: 01/25/2023] Open
Abstract
The rapid and accurate diagnosis of patients with minimally invasive procedures was once only found in science fiction. However, the discovery of extracellular vesicles (EVs) and their near ubiquity in body fluids, coupled with the advent of inexpensive next generation sequencing techniques and EV purification protocols, promises to make science fiction a reality. Purifying and sequencing the RNA content of EV from routine blood draws and urine samples are likely to enable pathologists and physicians to diagnose and track the progress of diseases in many inaccessible tissues in the near future. Here we present the evolutionary background of EV, summarize the biology of EV formation and cargo selection, and discuss the current barriers to making continuous liquid biopsies through the use of EV a science reality.
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Affiliation(s)
- Don Armstrong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Derek E Wildman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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24
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Hui L, Tong S, Kaitu'u-Lino TJ, Hannan NJ. A comparison of sample collection methods for quantifying cell-free fetal neurodevelopment transcripts in amniotic fluid. BMC Res Notes 2016; 9:335. [PMID: 27389196 PMCID: PMC4937574 DOI: 10.1186/s13104-016-2146-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023] Open
Abstract
Background Cell-free RNA (cfRNA) transcripts known to be expressed by the fetal brain are detectable by quantitative reverse transcription PCR (RT-qPCR) in amniotic fluid and represent potential biomarkers of neurodevelopment. The aim of this study was to compare the cfRNA yields from amniotic fluid (AF) collected in a commercial RNA stabilization product with the traditional method of freezing alone. Findings Thirteen women undergoing elective Cesarean birth at term without labor had whole AF collected at the time of uterine incision, prior to membrane rupture. Patient samples were split between Streck RNA blood collection tubes (BCT) and plain sterile polypropylene centrifuge tubes. Cell-free RNA from the AF supernatant was extracted according to a previously published protocol. RT qPCR was performed for the reference gene GAPDH, and three genes associated with neurodevelopment (NRXN3, NTRK3, and ZBTB18). The yield from samples collected in Streck RNA BCT and plain centrifuge tubes were compared with the paired t test. GAPDH, NRXN3 and ZBTB18 amplified successfully in all samples, but NTRK3 did not. The RNA yield was significantly lower in samples collected in the Streck RNA BCT compared with the traditional storage method of freezing alone for all three successfully amplified genes (p < 0.0001). Conclusions Selected cfRNA neurodevelopment transcripts are consistently detectable in third trimester AF. There appears to be no benefit in collecting AF in Streck RNA BCT for quantitative studies of AF cell-free RNA.
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Affiliation(s)
- Lisa Hui
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Rd, Heidelberg, VIC, 3084, Australia. .,Public Health Genetics, Murdoch Childrens Research Institute, Parkville, VIC, Australia.
| | - Stephen Tong
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Rd, Heidelberg, VIC, 3084, Australia
| | - Tu'Uhevaha J Kaitu'u-Lino
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Rd, Heidelberg, VIC, 3084, Australia
| | - Natalie J Hannan
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Rd, Heidelberg, VIC, 3084, Australia
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25
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Kalniņa Z, Meistere I, Kikuste I, Tolmanis I, Zayakin P, Linē A. Emerging blood-based biomarkers for detection of gastric cancer. World J Gastroenterol 2015; 21:11636-11653. [PMID: 26556992 PMCID: PMC4631966 DOI: 10.3748/wjg.v21.i41.11636] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 07/08/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023] Open
Abstract
Early detection and efficient monitoring of tumor dynamics are prerequisites for reducing disease burden and mortality, and for improving the management of patients with gastric cancer (GC). Blood-based biomarker assays for the detection of early-stage GC could be of great relevance both for population-wide or risk group-based screening programs, while circulating biomarkers that reflect the genetic make-up and dynamics of the tumor would allow monitoring of treatment efficacy, predict recurrences and assess the genetic heterogeneity of the tumor. Recent research to identify blood-based biomarkers of GC has resulted in the identification of a wide variety of cancer-associated molecules, including various proteins, autoantibodies against tumor associated antigens, cell-free DNA fragments, mRNAs and various non-coding RNAs, circulating tumor cells and cancer-derived extracellular vesicles. Each type of these biomarkers provides different information on the disease status, has different advantages and disadvantages, and distinct clinical usefulness. In the current review, we summarize the recent developments in blood-based GC biomarker discovery, discuss the origin of various types of biomarkers and their clinical usefulness and the technological challenges in the development of biomarker assays for clinical use.
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Isin M, Ozgur E, Cetin G, Erten N, Aktan M, Gezer U, Dalay N. Investigation of circulating lncRNAs in B-cell neoplasms. Clin Chim Acta. 2014;431:255-259. [PMID: 24583225 DOI: 10.1016/j.cca.2014.02.010] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNA) which are longer than 200 base pairs in length, play an important role in cellular machinery. Chronic lymphocytic leukemia (CLL) and multiple myeloma (MM) are neoplasms of B-cells. In our study we aimed to investigate circulating lncRNA levels of CLL and MM patients. For this purpose we selected 5 candidate lncRNAs (TUG1, LincRNA-p21, MALAT1, HOTAIR, and GAS5) where the first two are regulated by p53. Analyses were performed by real-time PCR using cDNA synthesized from plasma RNAs. In both disease groups differential levels of plasma lncRNAs were observed. LincRNA-p21 was the only molecule displaying significant changes in the CLL group while all remaining lncRNAs showed significant differences in the MM group. In the MM group only TUG1 showed higher levels than the healthy volunteers. In conclusion, the expression levels of the candidate lncRNA molecules display a general trend for tissue- and disease-specific expression which can provide important potential biomarkers specific to the particular disease type. However, further studies are necessary to elucidate their involvement in disease development and progression.
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