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Does Size Matter? Comparison of Extraction Yields for Different-Sized DNA Fragments by Seven Different Routine and Four New Circulating Cell-Free Extraction Methods. J Clin Microbiol 2018; 56:JCM.01061-18. [PMID: 30282788 DOI: 10.1128/jcm.01061-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022] Open
Abstract
An element essential for PCR detection of microbial agents in many sample types is the extraction step, designed to purify nucleic acids. Despite the importance of this step, yields have not been extensively compared across methods to determine whether the method used contributes to quantitative differences and the lack of commutability seen with existing clinical methods. This may in part explain why plasma and blood viral load assays have proven difficult to standardize. Also, studies have identified small DNA fragments of <200 bp in plasma (cell-free DNA [cfDNA]), which may include significant quantities of viral DNA. Our study evaluated extraction yields for 11 commercially available extraction methods, including 4 new methods designed to isolate cfDNA. Solutions of DNA fragments with sizes ranging from 50 to 1,500 bp were extracted, and then the eluates were tested by droplet digital PCR to determine the DNA fragment yield for each method. The results demonstrated a wide range of extraction yields across the variety of methods/instruments used, with the 50- and 100-bp fragment sizes showing especially inconsistent quantitative results and poor yields of less than 20%. Slightly higher, more consistent yields were seen with 2 of the 4 circulating cell-free extraction kits. These results demonstrate a significant need for further evaluation of nucleic acid yields across the variety of extraction platforms and highlight the poor extraction yields of small DNA fragments by existing methods. Further work is necessary to determine the impact of this inconsistency across instruments and the relevance of the low yields for smaller DNA fragments in clinical virology testing.
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Buckle G, Maranda L, Skiles J, Ong'echa JM, Foley J, Epstein M, Vik TA, Schroeder A, Lemberger J, Rosmarin A, Remick SC, Bailey JA, Vulule J, Otieno JA, Moormann AM. Factors influencing survival among Kenyan children diagnosed with endemic Burkitt lymphoma between 2003 and 2011: A historical cohort study. Int J Cancer 2016; 139:1231-40. [PMID: 27136063 PMCID: PMC5489240 DOI: 10.1002/ijc.30170] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 04/19/2016] [Indexed: 12/23/2022]
Abstract
Discovering how to improve survival and establishing clinical reference points for children diagnosed with endemic Burkitt lymphoma (eBL) in resource-constrained settings has recaptured international attention. Using multivariate analyses, we evaluated 428 children with eBL in Kenya for age, gender, tumor stage, nutritional status, hemoglobin, lactate dehydrogenase (LDH), Epstein-Barr virus (EBV) and Plasmodium falciparum prior to induction of chemotherapy (cyclophosphamide, vincristine, methotrexate and doxorubicin) to identify predictive and prognostic biomarkers of survival. During this 10 year prospective study period, 22% died in-hospital and 78% completed six-courses of chemotherapy. Of those, 16% relapsed or died later; 31% achieved event-free-survival; and 31% were lost to follow-up; the overall one-year survival was 45%. After adjusting for covariates, low hemoglobin (<8 g/dL) and high LDH (>400 mU/ml) were associated with increased risk of death (adjusted Hazard Ratio (aHR) = 1.57 [0.97-2.41]) and aHR = 1.84, [0.91-3.69], respectively). Anemic children with malaria were 3.55 times more likely to die [1.10-11.44] compared to patients without anemia or malarial infection. EBV load did not differ by tumor stage nor was it associated with survival. System-level factors can also contribute to poor outcomes. Children were more likely to die when inadvertently overdosed by more than 115% of the correct dose of cyclophosphamide (a HR = 1.43 [0.84-2.43]) or doxorubicin (a HR = 1.25, [0.66-2.35]), compared with those receiving accurate doses of the respective agent in this setting. This study codifies risk factors associated with poor outcomes for eBL patients in Africa and provides a benchmark by which to assess improvements in survival for new chemotherapeutic approaches.
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Affiliation(s)
- Geoffrey Buckle
- Molecular Medicine, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655
| | - Louise Maranda
- Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North, ASC6.1063, Worcester, MA 01655
| | - Jodi Skiles
- Pediatrics, Hemotology/Oncology, Indiana University School of Medicine, Full address: 705 Riley Hospital Drive, RI 2629, Indianapolis, IN 46202
| | - John Michael Ong'echa
- Center for Global, Health Research Kenya Medical Research Institute, P. O. Box 1578-40100, Kisumu, Kenya
| | - Joslyn Foley
- Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St. Biotech 2, Suite 318, Worcester, MA 01605
| | - Mara Epstein
- Quantitative Health Sciences, University of Massachusetts Medical School, 365 Plantation St. Biotech 1, Suite 100, Worcester, MA 01605
| | - Terry A. Vik
- Pediatrics, Hemotology/Oncology, Indiana University School of Medicine, Full address: 705 Riley Hospital Drive, ROC 4340, Indianapolis, IN 46202
| | | | | | - Alan Rosmarin
- Medicine, Hematology/Oncology, University of Massachusetts Medical School, 55 Lake Avenue North, H8-533, Worcester, MA 01655
| | - Scot C. Remick
- Physician Leader, Oncology and Senior Scientist, Maine Medical Center and Maine Medical Center Research Institute, Portland, ME 04074
| | - Jeffrey A. Bailey
- Medicine, Bioinformatics, University of Massachusetts Medical School, 55 Lake Avenue North, ASC4.1077, Worcester, MA 01655
| | - John Vulule
- Center for Global Health Research, Kenya Medical Research Institute, P. O. Box 1578-40100, Kisumu, Kenya
| | - Juliana A. Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Kenya Ministry of Health, P.O. Box 849-40100, Kisumu, Kenya
| | - Ann M. Moormann
- Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Biotech 2, Suite 318, Worcester MA, 01605 USA
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Kanakry J, Ambinder R. The Biology and Clinical Utility of EBV Monitoring in Blood. Curr Top Microbiol Immunol 2015; 391:475-99. [PMID: 26428386 DOI: 10.1007/978-3-319-22834-1_17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epstein-Barr virus (EBV) DNA in blood can be quantified in peripheral blood mononuclear cells, in circulating cell-free (CCF) DNA specimens, or in whole blood. CCF viral DNA may be actively released or extruded from viable cells, packaged in virions or passively shed from cells during apoptosis or necrosis. In infectious mononucleosis, viral DNA is detected in each of these kinds of specimens, although it is only transiently detected in CCF specimens. In nasopharyngeal carcinoma, CCF EBV DNA is an established tumor marker. In EBV-associated Hodgkin lymphoma and in EBV-associated extranodal NK-/T-cell lymphoma, there is growing evidence for the utility of CCF DNA as a tumor marker.
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Affiliation(s)
- Jennifer Kanakry
- Department of Oncology, Johns Hopkins School of Medicine, 389 CRB1 1650 Orleans, Baltimore, MD, 21287, USA
| | - Richard Ambinder
- Department of Oncology, Johns Hopkins School of Medicine, 389 CRB1 1650 Orleans, Baltimore, MD, 21287, USA.
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Chugh PE, Sin SH, Ozgur S, Henry DH, Menezes P, Griffith J, Eron JJ, Damania B, Dittmer DP. Systemically circulating viral and tumor-derived microRNAs in KSHV-associated malignancies. PLoS Pathog 2013; 9:e1003484. [PMID: 23874201 PMCID: PMC3715412 DOI: 10.1371/journal.ppat.1003484] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 05/24/2013] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are stable, small non-coding RNAs that modulate many downstream target genes. Recently, circulating miRNAs have been detected in various body fluids and within exosomes, prompting their evaluation as candidate biomarkers of diseases, especially cancer. Kaposi's sarcoma (KS) is the most common AIDS-associated cancer and remains prevalent despite Highly Active Anti-Retroviral Therapy (HAART). KS is caused by KS-associated herpesvirus (KSHV), a gamma herpesvirus also associated with Primary Effusion Lymphoma (PEL). We sought to determine the host and viral circulating miRNAs in plasma, pleural fluid or serum from patients with the KSHV-associated malignancies KS and PEL and from two mouse models of KS. Both KSHV-encoded miRNAs and host miRNAs, including members of the miR-17–92 cluster, were detectable within patient exosomes and circulating miRNA profiles from KSHV mouse models. Further characterization revealed a subset of miRNAs that seemed to be preferentially incorporated into exosomes. Gene ontology analysis of signature exosomal miRNA targets revealed several signaling pathways that are known to be important in KSHV pathogenesis. Functional analysis of endothelial cells exposed to patient-derived exosomes demonstrated enhanced cell migration and IL-6 secretion. This suggests that exosomes derived from KSHV-associated malignancies are functional and contain a distinct subset of miRNAs. These could represent candidate biomarkers of disease and may contribute to the paracrine phenotypes that are a characteristic of KS. Circulating microRNAs (miRNAs), such as those found in exosomes, have emerged as diagnostic tools and hold promise as minimally invasive, stable biomarkers. Transfer of tumor-derived exosomal miRNAs to surrounding cells may be an important form of cellular communication. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS), the most common AIDS-defining cancer worldwide. Here, we survey systemically circulating miRNAs and reveal potential biomarkers for KS and Primary Effusion Lymphoma (PEL). This expands previous tissue culture studies by profiling clinical samples and by using two new mouse models of KSHV tumorigenesis. Profiling of circulating miRNAs revealed that oncogenic and viral miRNAs were present in exosomes from KS patient plasma, pleural effusions and mouse models of KS. Analysis of human oncogenic miRNAs, including the well-known miR-17-92 cluster, revealed that several miRNAs were preferentially incorporated into exosomes in our KS mouse model. Gene ontology analysis of upregulated miRNAs showed that the majority of pathways affected were known targets of KSHV signaling pathways. Transfer of these oncogenic exosomes to immortalized hTERT-HUVEC cells enhanced cell migration and IL-6 secretion. These circulating miRNAs and KS derived exosomes may therefore be part of the paracrine signaling mechanism that mediates KSHV pathogenesis.
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MESH Headings
- Animals
- Biomarkers/blood
- Biomarkers/metabolism
- Body Fluids/metabolism
- Body Fluids/virology
- Cell Line
- Cell Movement
- Cells, Cultured
- Disease Models, Animal
- Endothelial Cells/metabolism
- Endothelial Cells/virology
- Exosomes/metabolism
- Exosomes/ultrastructure
- Exosomes/virology
- Gene Expression Profiling
- Herpesvirus 8, Human/isolation & purification
- Herpesvirus 8, Human/metabolism
- Humans
- Interleukin-6/metabolism
- Mice
- MicroRNAs/blood
- MicroRNAs/metabolism
- Pleural Cavity
- Pleural Effusion, Malignant/etiology
- RNA, Neoplasm/blood
- RNA, Neoplasm/metabolism
- RNA, Viral/blood
- RNA, Viral/metabolism
- Sarcoma, Kaposi/diagnosis
- Sarcoma, Kaposi/metabolism
- Sarcoma, Kaposi/physiopathology
- Sarcoma, Kaposi/virology
- Up-Regulation
- Viral Load
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Affiliation(s)
- Pauline E. Chugh
- Lineberger Comprehensive Cancer Center, Program in Global Oncology, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sang-Hoon Sin
- Lineberger Comprehensive Cancer Center, Program in Global Oncology, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sezgin Ozgur
- Lineberger Comprehensive Cancer Center, Program in Global Oncology, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David H. Henry
- Department of Oncology, Joan Karnell Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Prema Menezes
- Department of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jack Griffith
- Lineberger Comprehensive Cancer Center, Program in Global Oncology, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joseph J. Eron
- Department of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Blossom Damania
- Lineberger Comprehensive Cancer Center, Program in Global Oncology, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Dirk P. Dittmer
- Lineberger Comprehensive Cancer Center, Program in Global Oncology, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Abstract
This article discusses the molecular targets and the methods for identification of human papillomavirus and the human gammaherpesviruses, Epstein-Barr virus and human herpesvirus type 8.
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Affiliation(s)
- Travis Henry
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Wittson Hall, Room 4039, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
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