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Shim SM, Lee M, Jeon JP. Assessment of the Impact of Preanalytical DNA Integrity on the Genome Data Quality. Biopreserv Biobank 2024. [PMID: 38563611 DOI: 10.1089/bio.2023.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Many molecular approaches have been employed for the quality control (QC) of biobanked DNA samples. Since 2003, the National Biobank of Korea (NBK) has provided various studies with over half a million quality-controlled genomic DNA samples using conventional agarose gel electrophoresis and spectrophotometry. We assessed the postanalytical genomic data quality of DNA samples (n = 41) with a different range of the DNA quality index such as genomic quality number (GQN) for developing an evidence-based best practice for DNA quality criteria. We examined the quality indices of three different platforms, including single nucleotide polymorphism arrays, methylation arrays, and next-generation sequencing, using the same DNA samples (n = 41) of different quality, ranging from 4.0 to 10.0 values of the GQN. Our data analysis revealed that higher GQN value and/or double-stranded DNA concentration resulted in higher quality genomic data. In addition, all the analyzed DNA samples successfully generated good-quality genomic data. This study provides a guide for the QC of biobanked DNA samples for genomic analysis platforms.
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Affiliation(s)
- Sung-Mi Shim
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Meehee Lee
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Jae-Pil Jeon
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
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2
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Kopfnagel V, Klopp N, Bernemann I, Nizhegorodtseva N, Wilson R, Gronauer R, Seifert M, Illig T. Effects of Repeated Freeze and Thaw Cycles on the Genome-Wide DNA Methylation Profile of Isolated Genomic DNA. Biopreserv Biobank 2024; 22:110-114. [PMID: 37074140 DOI: 10.1089/bio.2022.0045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
The characterization of DNA methylation patterns to identify epigenetic markers for complex human diseases is an important and rapidly evolving part in biomedical research. DNA samples collected and stored in clinical biobanks over the past years are an important source for future epigenetic studies. Isolated gDNA is considered stable when stored at low temperatures for several years. However, the effect of multiple use and the associated repeated thawing of long-term stored DNA samples on DNA methylation patterns has not yet been investigated. In this study, we examined the influence of up to 10 freeze and thaw cycles on global DNA methylation by comparing genome-wide methylation profiles. DNA samples from 19 healthy volunteers were either frozen at -80°C or subjected to up to 10 freeze and thaw cycles. Genome-wide DNA methylation was analyzed after 0, 1, 3, 5, or 10 thaw cycles using the Illumina Infinium MethylationEPIC BeadChip. Evaluation of the global DNA methylation profile by beta-value density plots and multidimensional scaling plots revealed an expected clear participant-dependent variability, but a very low variability depending on the freeze and thaw cycles. In accordance, no significant difference in any of the methylated cytosine/guanine sites studied could be detected in the performed statistical analyses. Our results suggest that long-term frozen DNA samples are still suitable for epigenetic studies after multiple thaw cycles.
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Affiliation(s)
- Verena Kopfnagel
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Norman Klopp
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Inga Bernemann
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | | | - Rory Wilson
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
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3
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Faust H, Duffek P, Hentschel J, Popp D. Evaluation of Automated Magnetic Bead-Based DNA Extraction for Detection of Short Tandem Repeat Expansions With Nanopore Sequencing. J Clin Lab Anal 2024; 38:e25029. [PMID: 38506401 PMCID: PMC10997813 DOI: 10.1002/jcla.25029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/05/2024] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Long-read technologies such as nanopore sequencing provide new opportunities to detect short tandem repeat expansions. Therefore, a DNA extraction method is necessary that minimizes DNA fragmentation and hence allows the identification of large repeat expansions. In this study, an automated magnetic bead-based DNA extraction method and the required EDTA blood storage conditions as well as DNA and sequencing quality were evaluated for their suitability for repeat expansion detection with nanopore sequencing. METHODS DNA was extracted from EDTA blood, and subsequently, its concentration, purity, and integrity were assessed. DNA was then subjected to nanopore sequencing, and quality metrics of the obtained sequencing data were evaluated. RESULTS DNA extracted from fresh EDTA blood as well as from cooled or frozen EDTA blood revealed high DNA integrity whereas storage at room temperature over 7 days had detrimental effects. After nanopore sequencing, the read length N50 values of approximately 9 kb were obtained, and based on adaptive sampling of samples with a known repeat expansion, repeat expansions up to 10 kb could be detected. CONCLUSION The automated magnetic bead-based DNA extraction was sufficient to detect short tandem repeat expansions, omitting the need for high-molecular-weight DNA extraction methods. Therefore, DNA should be extracted either from fresh blood or from blood stored in cooled or frozen conditions. Consequently, this study may help other laboratories to evaluate their DNA extraction method regarding the suitability for detecting repeat expansions with nanopore sequencing.
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Affiliation(s)
- Helene Faust
- Institute of Human GeneticsUniversity of Leipzig Medical CenterLeipzigGermany
| | - Patricia Duffek
- Institute of Human GeneticsUniversity of Leipzig Medical CenterLeipzigGermany
| | - Julia Hentschel
- Institute of Human GeneticsUniversity of Leipzig Medical CenterLeipzigGermany
| | - Denny Popp
- Institute of Human GeneticsUniversity of Leipzig Medical CenterLeipzigGermany
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4
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Misra A, Powell EA. Preanalytical Challenges of Molecular Microbiology Tests. Clin Lab Med 2024; 44:33-43. [PMID: 38280796 DOI: 10.1016/j.cll.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
As infectious disease diagnostics increasingly incorporates molecular techniques, there are unique preanalytical concerns that must be considered. First, noninvasive specimen types that may be inadequate for culture-based diagnostics may be acceptable when using molecular tests. Second, specimen containers must be evaluated for the presence of substances that may interfere with amplification or sequencing reactions. Finally, the capacity of transport, storage, and processing conditions to maintain nucleic acid integrity and avoid contamination must be assessed. This review explores these issues and the effects they may have on result quality.
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Affiliation(s)
- Anisha Misra
- Department of Laboratory Medicine, Cleveland Clinic, Robert J. Tomsich Pathology and Laboratory Medicine Institute, 10300 Carnegie Avenue LL-1, Cleveland, OH 44195, USA
| | - Eleanor A Powell
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, 3188 Bellevue Avenue, Cincinnati, OH 45219, USA.
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Faigle W, Piccirelli M, Hortobágyi T, Frontzek K, Cannon AE, Zürrer WE, Granberg T, Kulcsar Z, Ludersdorfer T, Frauenknecht KBM, Reimann R, Ineichen BV. The Brainbox -a tool to facilitate correlation of brain magnetic resonance imaging features to histopathology. Brain Commun 2023; 5:fcad307. [PMID: 38025281 PMCID: PMC10664401 DOI: 10.1093/braincomms/fcad307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/20/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Magnetic resonance imaging (MRI) has limitations in identifying underlying tissue pathology, which is relevant for neurological diseases such as multiple sclerosis, stroke or brain tumours. However, there are no standardized methods for correlating MRI features with histopathology. Thus, here we aimed to develop and validate a tool that can facilitate the correlation of brain MRI features to corresponding histopathology. For this, we designed the Brainbox, a waterproof and MRI-compatible 3D printed container with an integrated 3D coordinate system. We used the Brainbox to acquire post-mortem ex vivo MRI of eight human brains, fresh and formalin-fixed, and correlated focal imaging features to histopathology using the built-in 3D coordinate system. With its built-in 3D coordinate system, the Brainbox allowed correlation of MRI features to corresponding tissue substrates. The Brainbox was used to correlate different MR image features of interest to the respective tissue substrate, including normal anatomical structures such as the hippocampus or perivascular spaces, as well as a lacunar stroke. Brain volume decreased upon fixation by 7% (P = 0.01). The Brainbox enabled degassing of specimens before scanning, reducing susceptibility artefacts and minimizing bulk motion during scanning. In conclusion, our proof-of-principle experiments demonstrate the usability of the Brainbox, which can contribute to improving the specificity of MRI and the standardization of the correlation between post-mortem ex vivo human brain MRI and histopathology. Brainboxes are available upon request from our institution.
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Affiliation(s)
- Wolfgang Faigle
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Marco Piccirelli
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
| | - Tibor Hortobágyi
- Institute of Neuropathology, University of Zurich, CH-8091 Zurich, Switzerland
| | - Karl Frontzek
- Institute of Neuropathology, University of Zurich, CH-8091 Zurich, Switzerland
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, WC1N 1PJ London, United Kingdom
| | - Amelia Elaine Cannon
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
| | - Wolfgang Emanuel Zürrer
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
| | - Tobias Granberg
- Department of Neuroradiology, Karolinska University Hospital, S-141 86 Stockholm, Sweden
| | - Zsolt Kulcsar
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
| | - Thomas Ludersdorfer
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Katrin B M Frauenknecht
- Institute of Neuropathology, University of Zurich, CH-8091 Zurich, Switzerland
- Luxembourg Center of Neuropathology (LCNP), Laboratoire National de Santé, 3555 Dudelange, Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé, 3555 Dudelange, Luxembourg
| | - Regina Reimann
- Institute of Neuropathology, University of Zurich, CH-8091 Zurich, Switzerland
| | - Benjamin Victor Ineichen
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
- Center for Reproducible Science, University of Zurich, CH-8001 Zurich, Switzerland
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6
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Chen YY, Han QY, Chen QY, Zhou WJ, Zhang JG, Zhang X, Lin A. Impact of Sample Processing and Storage Conditions on RNA Quality of Fresh-Frozen Cancer Tissues. Biopreserv Biobank 2023; 21:510-517. [PMID: 37040277 DOI: 10.1089/bio.2022.0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Background: A biobank is a central resource that supports basic and clinical research. RNA quality of fresh-frozen tissue specimens in the biobank is highly associated with the success of downstream applications. Therefore, it is very important to evaluate the impact of tissue processing and storage conditions on RNA quality. Methods: A total of 238 surgically removed tissue specimens, including esophagus, lung, liver, stomach, colon, and rectal cancer, were used to evaluate RNA quality. Two tissue homogenization methods, manual and TissueLyser, were compared and the impacts of temperature fluctuation, tissue types, storage period, and clinicopathological parameters on RNA quality were analyzed. Results: RNA integrity was not influenced by tissue homogenization methods and tissue types. However, RNA integrity number (RIN) values were significantly correlated with temperature fluctuation. When the power of a -80°C freezer was cut off, RNA integrity of frozen tissues was not significantly affected until the temperature increased to 0°C. When the temperature rose to room temperature and remained for 4 hours, RNA integrity was almost completely destroyed. In addition, various cancer tissues with short-term storage at -80°C (<5 years) or high tumor differentiation had higher RINs. Conclusions: Tissue processing and storage conditions affected RNA quality of fresh-frozen cancer tissues. It is necessary to keep storage temperature stable and keep specimens at ultralow temperatures during homogenization. Also, for a biobank containing multiple types of cancer tissue samples, it is better to store them in liquid nitrogen if the storage duration is more than 5 years.
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Affiliation(s)
- Yuan-Yuan Chen
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Qiu-Yue Han
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Qiong-Yuan Chen
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Wen-Jun Zhou
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Jian-Gang Zhang
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Xia Zhang
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Aifen Lin
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
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Lee NY, Hum M, Tan GP, Seah AC, Kin PT, Tan NC, Law HY, Lee ASG. Degradation of methylation signals in cryopreserved DNA. Clin Epigenetics 2023; 15:147. [PMID: 37697422 PMCID: PMC10496221 DOI: 10.1186/s13148-023-01565-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Blood-based DNA methylation has shown great promise as a biomarker in a wide variety of diseases. Studies of DNA methylation in blood often utilize samples which have been cryopreserved for years or even decades. Therefore, changes in DNA methylation associated with long-term cryopreservation can introduce biases or otherwise mislead methylation analyses of cryopreserved DNA. However, previous studies have presented conflicting results with studies reporting hypomethylation, no effect, or even hypermethylation of DNA following long-term cryopreservation. These studies may have been limited by insufficient sample sizes, or by their profiling of methylation only on an aggregate global scale, or profiling of only a few CpGs. RESULTS We analyzed two large prospective cohorts: a discovery (n = 126) and a validation (n = 136) cohort, where DNA was cryopreserved for up to four years. In both cohorts there was no detectable change in mean global methylation across increasing storage durations as DNA. However, when analysis was performed on the level of individual CpG methylation both cohorts exhibited a greater number of hypomethylated than hypermethylated CpGs at q-value < 0.05 (4049 hypomethylated but only 50 hypermethylated CpGs in discovery, and 63 hypomethylated but only 6 hypermethylated CpGs in validation). The results were the same even after controlling for age, storage duration as buffy coat prior to DNA extraction, and estimated cell type composition. Furthermore, we find that in both cohorts, CpGs have a greater likelihood to be hypomethylated the closer they are to a CpG island; except for CpGs at the CpG islands themselves which are less likely to be hypomethylated. CONCLUSION Cryopreservation of DNA after a few years results in a detectable bias toward hypomethylation at the level of individual CpG methylation, though when analyzed in aggregate there is no detectable change in mean global methylation. Studies profiling methylation in cryopreserved DNA should be mindful of this hypomethylation bias, and more attention should be directed at developing more stable methods of DNA cryopreservation for biomedical research or clinical use.
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Affiliation(s)
- Ning Yuan Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Melissa Hum
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Guek Peng Tan
- DNA Diagnostic and Research Laboratory, KK Women's and Children's Hospital, 100 Bukit Timah Rd, Singapore, 229899, Singapore
| | - Ai Choo Seah
- SingHealth Polyclinics, 167 Jalan Bukit Merah, Singapore, 150167, Singapore
| | - Patricia T Kin
- SingHealth Polyclinics, 167 Jalan Bukit Merah, Singapore, 150167, Singapore
| | - Ngiap Chuan Tan
- SingHealth Polyclinics, 167 Jalan Bukit Merah, Singapore, 150167, Singapore
- SingHealth Duke-NUS Family Medicine Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Hai-Yang Law
- DNA Diagnostic and Research Laboratory, KK Women's and Children's Hospital, 100 Bukit Timah Rd, Singapore, 229899, Singapore
| | - Ann S G Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore.
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117593, Singapore.
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8
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Kavita U, Sun K, Braun M, Lembke W, Mody H, Kamerud J, Yang TY, Braun IV, Fang X, Gao W, Gupta S, Hofer M, Liao MZ, Loo L, McBlane F, Menochet K, Stubenrauch KG, Upreti VV, Vigil A, Wiethoff CM, Xia CQ, Zhu X, Jawa V, Chemuturi N. PK/PD and Bioanalytical Considerations of AAV-Based Gene Therapies: an IQ Consortium Industry Position Paper. AAPS J 2023; 25:78. [PMID: 37523051 DOI: 10.1208/s12248-023-00842-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Interest and efforts to use recombinant adeno-associated viruses (AAV) as gene therapy delivery tools to treat disease have grown exponentially. However, gaps in understanding of the pharmacokinetics/pharmacodynamics (PK/PD) and disposition of this modality exist. This position paper comes from the Novel Modalities Working Group (WG), part of the International Consortium for Innovation and Quality in Pharmaceutical Development (IQ). The pan-industry WG effort focuses on the nonclinical PK and clinical pharmacology aspects of AAV gene therapy and related bioanalytical considerations.Traditional PK concepts are generally not applicable to AAV-based therapies due to the inherent complexity of a transgene-carrying viral vector, and the multiple steps and analytes involved in cell transduction and transgene-derived protein expression. Therefore, we explain PK concepts of biodistribution of AAV-based therapies and place key terminologies related to drug exposure and PD in the proper context. Factors affecting biodistribution are presented in detail, and guidelines are provided to design nonclinical studies to enable a stage-gated progression to Phase 1 testing. The nonclinical and clinical utility of transgene DNA, mRNA, and protein analytes are discussed with bioanalytical strategies to measure these analytes. The pros and cons of qPCR vs. ddPCR technologies for DNA/RNA measurement and qualitative vs. quantitative methods for transgene-derived protein are also presented. Last, best practices and recommendations for use of clinical and nonclinical data to project human dose and response are discussed. Together, the manuscript provides a holistic framework to discuss evolving concepts of PK/PD modeling, bioanalytical technologies, and clinical dose selection in gene therapy.
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Affiliation(s)
- Uma Kavita
- Spark Therapeutics, Inc., Philadelphia, Pennsylvania, 19104, USA.
| | - Kefeng Sun
- Takeda Development Center Americas Inc., 125 Binney St, Cambridge, Massachusetts, 02142, USA.
| | - Manuela Braun
- Bayer AG, Pharmaceuticals R&D, 13342, Berlin, Germany
| | - Wibke Lembke
- Integrated Biologix GmbH, 4051, Basel, Switzerland
| | - Hardik Mody
- Genentech Inc., South San Francisco, California, USA
| | | | - Tong-Yuan Yang
- Janssen R&D LLC., Spring House, Pennsylvania, 19477, USA
| | | | - Xiaodong Fang
- Asklepios BioPharmaceutical, Inc., Research Triangle, North Carolina, 27709, USA
| | - Wei Gao
- EMD Serono Research & Development Institute, Inc., Billerica, Massachusetts, 01821, USA
| | - Swati Gupta
- AbbVie, 2525 Dupont Drive, Irvine, California, 92612, USA
| | - Magdalena Hofer
- Spark Therapeutics, Inc., Philadelphia, Pennsylvania, 19104, USA
| | | | - LiNa Loo
- Vertex Pharmaceuticals Boston, Boston, Massachusetts, 02210, USA
| | | | | | | | | | - Adam Vigil
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, 06877, USA
| | | | - Cindy Q Xia
- ReNAgade Therapeutics, Cambridge, Massachusetts, 02142, USA
| | - Xu Zhu
- AstraZeneca, Waltham, Massachusetts, 02451, USA
| | - Vibha Jawa
- Bristol Myers Squibb, Lawrence Township, New Jersey, 08648, USA
| | - Nagendra Chemuturi
- Takeda Development Center Americas Inc., 125 Binney St, Cambridge, Massachusetts, 02142, USA
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Ferdousi T, Dutta AK, Chowdhury MAH, Islam K, Islam MT, Islam MZ, Bulbul MRH, Khan AI, Qadri F. Role of TaqMan array card in determining causative organisms of acute febrile illness in hospitalized patients. J Clin Lab Anal 2023; 37:e24948. [PMID: 37496432 PMCID: PMC10492456 DOI: 10.1002/jcla.24948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/23/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Acute febrile illness (AFI) is a prevalent disease in developing countries that is difficult to diagnose due to the diversity of infectious organisms and the poor quality of clinical diagnosis. TaqMan array card (TAC) can detect up to 35 AFI-associated organisms in 1.5 h, addressing diagnostic demands. In this study, we aimed to evaluate the role of TAC in determining the causative organisms in hospitalized AFI patients. METHODS The study had a cross-sectional design and enrolled 120 admitted patients with persistent fever for three or more days from the medicine ward of Chittagong Medical College Hospital (CMCH) and Bangladesh Institute of Tropical and Infectious Diseases Hospital (BITID). Blood samples were collected and then subjected to automated BacT/Alert blood culture, microbial culture, TAC assay, and typhoid/paratyphoid test. RESULTS The total number of study participants was 120, among them 48 (40%) samples showed a positive result in TAC card, 29 (24.16%) were TP positive and nine (7.51%) were culture positive. The number of organisms detected by the TAC card was 13 bacteria, three viruses, one protozoan, and one fungus. The sensitivity and specificity of the TAC assay for different bacterial pathogen compared to blood culture was 44.44%, and 90.99%, respectively. In contrast, the TP test had a sensitivity and specificity of 100% and 80%, respectively, compared to the blood culture test. CONCLUSION TAC can be a handful tool for detecting multiple organisms in AFI with high specificity which can facilitate early diagnosis of different pathogens contributing to AFI.
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Affiliation(s)
- Tabassum Ferdousi
- Bangladesh Institute of Tropical and Infectious DiseasesChattogramBangladesh
| | | | | | - Kamrul Islam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)DhakaBangladesh
| | - Md. Taufiqul Islam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)DhakaBangladesh
| | - Md. Zahirul Islam
- Institute for Developing Science and Health Initiatives (ideSHi)DhakaBangladesh
| | | | - Ashraful Islam Khan
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)DhakaBangladesh
| | - Firdausi Qadri
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)DhakaBangladesh
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10
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Hanin A, Cespedes J, Pulluru Y, Gopaul M, Aronica E, Decampo D, Helbig I, Howe CL, Huttner A, Koh S, Navarro V, Taraschenko O, Vezzani A, Wilson MR, Xian J, Gaspard N, Hirsch LJ. Review and standard operating procedures for collection of biospecimens and analysis of biomarkers in new onset refractory status epilepticus. Epilepsia 2023; 64:1444-1457. [PMID: 37039049 PMCID: PMC10756682 DOI: 10.1111/epi.17600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
New onset refractory status epilepticus (NORSE), including its subtype with a preceding febrile illness known as febrile infection-related epilepsy syndrome (FIRES), is one of the most severe forms of status epilepticus. The exact causes of NORSE are currently unknown, and there is so far no disease-specific therapy. Identifying the underlying pathophysiology and discovering specific biomarkers, whether immunologic, infectious, genetic, or other, may help physicians in the management of patients with NORSE. A broad spectrum of biomarkers has been proposed for status epilepticus patients, some of which were evaluated for patients with NORSE. Nonetheless, none has been validated, due to significant variabilities in study cohorts, collected biospecimens, applied analytical methods, and defined outcome endpoints, and to small sample sizes. The NORSE Institute established an open NORSE/FIRES biorepository for health-related data and biological samples allowing the collection of biospecimens worldwide, promoting multicenter research and sharing of data and specimens. Here, we suggest standard operating procedures for biospecimen collection and biobanking in this rare condition. We also propose criteria for the appropriate use of previously collected biospecimens. We predict that the widespread use of standardized procedures will reduce heterogeneity, facilitate the future identification of validated biomarkers for NORSE, and provide a better understanding of the pathophysiology and best clinical management for these patients.
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Affiliation(s)
- Aurélie Hanin
- Department of Neurology and Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Sorbonne Université, Institut du Cerveau ICM, Paris Brain Institute, Inserm, CNRS, Assistance Publique -Hôpitaux de Paris, Hôpital de la Pitié-Salpêtrière, DMU Neurosciences 6, Paris, France
- Assistance Publique -Hôpitaux de Paris, Hôpital de la Pitié-Salpêtrière, DMU Neurosciences 6, Epilepsy Unit and Department of Clinical Neurophysiology, Paris, France
| | - Jorge Cespedes
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
- Universidad Autonoma de Centro America, School of Medicine, San Jose, Costa Rica
| | - Yashwanth Pulluru
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
- Nebraska Medical Center, Omaha, Nebraska, USA
| | - Margaret Gopaul
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Danielle Decampo
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Charles L. Howe
- Division of Experimental Neurology, Mayo Clinic, Rochester, Minnesota, USA
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Anita Huttner
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sookyong Koh
- Department of Pediatrics, Children’s Hospital Medical Center, University of Nebraska, Omaha, Nebraska, USA
| | - Vincent Navarro
- Sorbonne Université, Institut du Cerveau ICM, Paris Brain Institute, Inserm, CNRS, Assistance Publique -Hôpitaux de Paris, Hôpital de la Pitié-Salpêtrière, DMU Neurosciences 6, Paris, France
- Assistance Publique -Hôpitaux de Paris, Hôpital de la Pitié-Salpêtrière, DMU Neurosciences 6, Epilepsy Unit and Department of Clinical Neurophysiology, Paris, France
| | - Olga Taraschenko
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Annamaria Vezzani
- Department of Acute Brain Injury, Istituto di Recerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, California, San Francisco, USA
| | - Julie Xian
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nicolas Gaspard
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
- Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Lawrence J. Hirsch
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
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11
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Conrad S, Gant Kanegusuku A, Conklin SE. Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics. Clin Biochem 2023; 115:22-32. [PMID: 36495954 PMCID: PMC9729171 DOI: 10.1016/j.clinbiochem.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Recent studies evaluating the preanalytical factors that impact the outcome of nucleic-acid based methods for the confirmation of SARS-CoV-2 have illuminated the importance of identifying variables that promoted accurate testing, while using scarce resources efficiently. The majority of laboratory errors occur in the preanalytical phase. While there are many resources identifying and describing mechanisms for main laboratory testing on automated platforms, there are fewer comprehensive resources for understanding important preanalytical and environmental factors that affect accurate molecular diagnostic testing of infectious diseases. This review identifies evidence-based factors that have been documented to impact the outcome of nucleic acid-based molecular techniques for the diagnosis of infectious diseases.
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Affiliation(s)
- Stephanie Conrad
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | | | - Steven E Conklin
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA; Department of Anatomic & Clinical Pathology, Tufts University School of Medicine, Boston, MA, USA.
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12
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Schulze Johann K, Bauer H, Wiegand P, Pfeiffer H, Vennemann M. Detecting DNA damage in stored blood samples. Forensic Sci Med Pathol 2023; 19:50-59. [PMID: 36355320 PMCID: PMC10014702 DOI: 10.1007/s12024-022-00549-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2022] [Indexed: 11/11/2022]
Abstract
Several commercially available quantitative real-time PCR (qPCR) systems enable highly sensitive detection of human DNA and provide a degradation index (DI) to assess DNA quality. From routine casework in forensic genetics, it was observed that DNA degradation in forensic samples such as blood samples stored under sub-optimal conditions leads to visible effects in multiplex analyses of short tandem repeat markers (STRs) due to decreased amplification efficiencies in longer amplicons. It was further noticed that degradation indices often remain below the value that is considered to be critical. Thus, the aim of this work was to systematically analyze this effect and to compare conventional qPCR assays with a modified qPCR approach using uracil DNA glycosylase (UNG) and DNA quality assessment methods based on electrophoresis. Blood samples were stored at three different storage temperatures for up to 316 days. Significantly increased DNA recovery was observed from samples stored at high temperatures (37 °C) compared samples stored at room temperature and 4 °C. We observed typical effects of degradation in STR analyses but no correlation between DI and storage time in any of the storage conditions. Adding UNG slightly increased the sensitivity of detecting DNA degradation in one of the qPCR kits used in this study. This observation was not confirmed when using a second qPCR system. Electrophoretic systems did also not reveal significant correlations between integrity values and time. Methods for detecting DNA degradation are usually limited to the detection of DNA fragmentation, and we conclude that degradation affecting forensic STR typing is more complex.
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Affiliation(s)
- Kristina Schulze Johann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany.
| | - Hannah Bauer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
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13
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Adedinsewo D, Hardway HD, Morales-Lara AC, Wieczorek MA, Johnson PW, Douglass EJ, Dangott BJ, Nakhleh RE, Narula T, Patel PC, Goswami RM, Lyle MA, Heckman AJ, Leoni-Moreno JC, Steidley DE, Arsanjani R, Hardaway B, Abbas M, Behfar A, Attia ZI, Lopez-Jimenez F, Noseworthy PA, Friedman P, Carter RE, Yamani M. Non-invasive detection of cardiac allograft rejection among heart transplant recipients using an electrocardiogram based deep learning model. EUROPEAN HEART JOURNAL. DIGITAL HEALTH 2023; 4:71-80. [PMID: 36974261 PMCID: PMC10039431 DOI: 10.1093/ehjdh/ztad001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/08/2022] [Indexed: 01/15/2023]
Abstract
Aims Current non-invasive screening methods for cardiac allograft rejection have shown limited discrimination and are yet to be broadly integrated into heart transplant care. Given electrocardiogram (ECG) changes have been reported with severe cardiac allograft rejection, this study aimed to develop a deep-learning model, a form of artificial intelligence, to detect allograft rejection using the 12-lead ECG (AI-ECG). Methods and results Heart transplant recipients were identified across three Mayo Clinic sites between 1998 and 2021. Twelve-lead digital ECG data and endomyocardial biopsy results were extracted from medical records. Allograft rejection was defined as moderate or severe acute cellular rejection (ACR) based on International Society for Heart and Lung Transplantation guidelines. The extracted data (7590 unique ECG-biopsy pairs, belonging to 1427 patients) was partitioned into training (80%), validation (10%), and test sets (10%) such that each patient was included in only one partition. Model performance metrics were based on the test set (n = 140 patients; 758 ECG-biopsy pairs). The AI-ECG detected ACR with an area under the receiver operating curve (AUC) of 0.84 [95% confidence interval (CI): 0.78-0.90] and 95% (19/20; 95% CI: 75-100%) sensitivity. A prospective proof-of-concept screening study (n = 56; 97 ECG-biopsy pairs) showed the AI-ECG detected ACR with AUC = 0.78 (95% CI: 0.61-0.96) and 100% (2/2; 95% CI: 16-100%) sensitivity. Conclusion An AI-ECG model is effective for detection of moderate-to-severe ACR in heart transplant recipients. Our findings could improve transplant care by providing a rapid, non-invasive, and potentially remote screening option for cardiac allograft function.
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Affiliation(s)
- Demilade Adedinsewo
- Department of Cardiovascular Medicine, Division of Cardiovascular Diseases, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224, USA
| | - Heather D Hardway
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Andrea Carolina Morales-Lara
- Department of Cardiovascular Medicine, Division of Cardiovascular Diseases, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224, USA
| | - Mikolaj A Wieczorek
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Patrick W Johnson
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Erika J Douglass
- Department of Cardiovascular Medicine, Division of Cardiovascular Diseases, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224, USA
| | - Bryan J Dangott
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL, USA
| | - Raouf E Nakhleh
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL, USA
| | - Tathagat Narula
- Department of Transplantation, Mayo Clinic, Jacksonville, FL, USA
| | - Parag C Patel
- Department of Transplantation, Mayo Clinic, Jacksonville, FL, USA
| | - Rohan M Goswami
- Department of Transplantation, Mayo Clinic, Jacksonville, FL, USA
| | - Melissa A Lyle
- Department of Transplantation, Mayo Clinic, Jacksonville, FL, USA
| | - Alexander J Heckman
- Department of Cardiovascular Medicine, Division of Cardiovascular Diseases, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224, USA
| | | | - D Eric Steidley
- Department of Cardiovascular Medicine, Mayo Clinic, Phoenix, AZ, USA
| | - Reza Arsanjani
- Department of Cardiovascular Medicine, Mayo Clinic, Phoenix, AZ, USA
| | - Brian Hardaway
- Department of Cardiovascular Medicine, Mayo Clinic, Phoenix, AZ, USA
| | - Mohsin Abbas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Atta Behfar
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Zachi I Attia
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Paul Friedman
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rickey E Carter
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Mohamad Yamani
- Department of Cardiovascular Medicine, Division of Cardiovascular Diseases, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224, USA
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14
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Lynton‐Jenkins JG, Chaine AS, Russell AF, Bonneaud C. Parasite detection and quantification in avian blood is dependent on storage medium and duration. Ecol Evol 2023; 13:e9819. [PMID: 36789332 PMCID: PMC9911630 DOI: 10.1002/ece3.9819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/12/2023] Open
Abstract
Studies of parasites in wild animal populations often rely on molecular methods to both detect and quantify infections. However, method accuracy is likely to be influenced by the sampling approach taken prior to nucleic acid extraction. Avian Haemosporidia are studied primarily through the screening of host blood, and a range of storage mediums are available for the short- to long-term preservation of samples. Previous research has suggested that storage medium choice may impact the accuracy of PCR-based parasite detection, however, this relationship has never been explicitly tested and may be exacerbated by the duration of sample storage. These considerations could also be especially critical for sensitive molecular methods used to quantify infection (qPCR). To test the effect of storage medium and duration on Plasmodium detection and quantification, we split blood samples collected from wild birds across three medium types (filter paper, Queen's lysis buffer, and 96% ethanol) and carried out DNA extractions at five time points (1, 6, 12, 24, and 36 months post-sampling). First, we found variation in DNA yield obtained from blood samples dependent on their storage medium which had subsequent negative impacts on both detection and estimates of Plasmodium copy number. Second, we found that detection accuracy (incidence of true positives) was highest for filter-paper-stored samples (97%), while accuracy for ethanol and Queen's lysis buffer-stored samples was influenced by either storage duration or extraction yield, respectively. Lastly, longer storage durations were associated with decreased copy number estimates across all storage mediums; equating to a 58% reduction between the first- and third-year post-sampling for lysis-stored samples. These results raise questions regarding the utility of standardizing samples by dilution, while also illustrating the critical importance of considering storage approaches in studies of Haemosporidia comparing samples subjected to different storage regimes and/or stored for varying lengths of time.
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Affiliation(s)
| | - Alexis S. Chaine
- Station for Theoretical and Experimental EcologyCNRSMoulisFrance
- Institute for Advanced Studies in ToulouseToulouseFrance
| | - Andrew F. Russell
- Centre for Ecology and ConservationUniversity of ExeterPenrynUK
- Station for Theoretical and Experimental EcologyCNRSMoulisFrance
| | - Camille Bonneaud
- Centre for Ecology and ConservationUniversity of ExeterPenrynUK
- Station for Theoretical and Experimental EcologyCNRSMoulisFrance
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15
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Wang Z, Chen L, Li Q, Zhang H, Shan Y, Qi L, Wang H, Chen Y. Association between single-nucleotide polymorphism rs145497186 related to NDUFV2 and lumbar disc degeneration: a pilot case–control study. J Orthop Surg Res 2022; 17:473. [PMID: 36309697 PMCID: PMC9618206 DOI: 10.1186/s13018-022-03368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/23/2022] [Indexed: 11/10/2022] Open
Abstract
Objective The association between the single-nucleotide polymorphisms (SNPs) rs28742109, rs12955018, rs987850, rs8093805, rs12965084 and rs145497186 related to gene named NADH dehydrogenase [ubiquinone] flavoprotein 2 (NDUFV2) and lumbar disc degeneration (LDD) was preliminary investigated in a small sample size.
Methods A total of 46 patients with LDD and 45 controls were recruited at Qilu Hospital of Shandong University, and each participant provided 5 mL peripheral venous blood. NA was extracted from the blood of each participant for further genotyping. The frequency of different genotypes in the case group and control group was determined, and analysis of the risk of LDD associated with different SNP genotypes was performed. The visual analogue scale (VAS) scores of the patients’ degree of chronic low back pain were calculated, and the relationship between VAS scores and SNPs was analysed.
Results After excluding the influence of sex, age, height, and weight on LDD, a significant association between SNP rs145497186 related to NDUFV2 and LDD persisted (P = 0.006). Simultaneously, rs145497186 was found to be associated with chronic low back pain in LDD populations.
Conclusion NDUFV2 rs145497186 SNP could be associated with susceptibility to LDD and the degree of chronic low back pain. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-022-03368-y.
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16
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Szigeti KA, Barták BK, Nagy ZB, Zsigrai S, Papp M, Márkus E, Igaz P, Takács I, Molnár B, Kalmár A. Methodological and Biological Factors Influencing Global DNA Methylation Results Measured by LINE-1 Pyrosequencing Assay in Colorectal Tissue and Liquid Biopsy Samples. Int J Mol Sci 2022; 23:ijms231911608. [PMID: 36232908 PMCID: PMC9569782 DOI: 10.3390/ijms231911608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1) bisulfite pyrosequencing is a widely used technique for genome-wide methylation analyses. We aimed to investigate the effects of experimental and biological factors on its results to improve the comparability. LINE-1 bisulfite pyrosequencing was performed on colorectal tissue (n = 222), buffy coat (n = 39), and plasma samples (n = 9) of healthy individuals and patients with colorectal tumors. Significantly altered methylation was observed between investigated LINE-1 CpG positions of non-tumorous tissues (p ≤ 0.01). Formalin-fixed, paraffin-embedded biopsies (73.0 ± 5.3%) resulted in lower methylation than fresh frozen samples (76.1 ± 2.8%) (p ≤ 0.01). DNA specimens after long-term storage showed higher methylation levels (+3.2%, p ≤ 0.01). In blood collection tubes with preservatives, cfDNA and buffy coat methylation significantly changed compared to K3EDTA tubes (p ≤ 0.05). Lower methylation was detected in older (>40 years, 76.8 ± 1.7%) vs. younger (78.1 ± 1.0%) female patients (p ≤ 0.05), and also in adenomatous tissues with MTHFR 677CT, or 1298AC mutations vs. wild-type (p ≤ 0.05) comparisons. Based on our findings, it is highly recommended to consider the application of standard DNA samples in the case of a possible clinical screening approach, as well as in experimental research studies.
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Affiliation(s)
- Krisztina A Szigeti
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-459-1500
| | - Barbara K Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Zsófia B Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Sára Zsigrai
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary
| | - Eszter Márkus
- Department of Anaesthesia and Intensive Care, Pest County Flor Ferenc Hospital, 2143 Kistarcsa, Hungary
| | - Peter Igaz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
- Department of Endocrinology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
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17
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Sarathkumara YD, Browne DJ, Kelly AM, Pattinson DJ, Rush CM, Warner J, Proietti C, Doolan DL. The Effect of Tropical Temperatures on the Quality of RNA Extracted from Stabilized Whole-Blood Samples. Int J Mol Sci 2022; 23:ijms231810609. [PMID: 36142559 PMCID: PMC9503649 DOI: 10.3390/ijms231810609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022] Open
Abstract
Whole-blood-derived transcriptional profiling is widely used in biomarker discovery, immunological research, and therapeutic development. Traditional molecular and high-throughput transcriptomic platforms, including molecular assays with quantitative PCR (qPCR) and RNA-sequencing (RNA-seq), are dependent upon high-quality and intact RNA. However, collecting high-quality RNA from field studies in remote tropical locations can be challenging due to resource restrictions and logistics of post-collection processing. The current study tested the relative performance of the two most widely used whole-blood RNA collection systems, PAXgene® and Tempus™, in optimal laboratory conditions as well as suboptimal conditions in tropical field sites, including the effects of extended storage times and high storage temperatures. We found that Tempus™ tubes maintained a slightly higher RNA quantity and integrity relative to PAXgene® tubes at suboptimal tropical conditions. Both PAXgene® and Tempus™ tubes gave similar RNA purity (A260/A280). Additionally, Tempus™ tubes preferentially maintained the stability of mRNA transcripts for two reference genes tested, Succinate dehydrogenase complex, subunit A (SDHA) and TATA-box-binding protein (TBP), even when RNA quality decreased with storage length and temperature. Both tube types preserved the rRNA transcript 18S ribosomal RNA (18S) equally. Our results suggest that Tempus™ blood RNA collection tubes are preferable to PAXgene® for whole-blood collection in suboptimal tropical conditions for RNA-based studies in resource-limited settings.
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Affiliation(s)
- Yomani D. Sarathkumara
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Daniel J. Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Ashton M. Kelly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - David J. Pattinson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Catherine M. Rush
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Jeffrey Warner
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Carla Proietti
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Denise L. Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- Correspondence:
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18
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Hamim I, Suzuki JY, Borth WB, Melzer MJ, Wall MM, Hu JS. Preserving plant samples from remote locations for detection of RNA and DNA viruses. Front Microbiol 2022; 13:930329. [PMID: 36090110 PMCID: PMC9453036 DOI: 10.3389/fmicb.2022.930329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Viral diseases in plants have a significant impact on agricultural productivity. Effective detection is needed to facilitate accurate diagnosis and characterization of virus infections essential for crop protection and disease management. For sensitive polymerase chain reaction (PCR)-based methods, it is important to preserve the integrity of nucleic acids in plant tissue samples. This is especially critical when samples are collected from isolated areas, regions distant from a laboratory, or in developing countries that lack appropriate facilities or equipment for diagnostic analyses. RNAlater® provides effective, reliable sample storage by stabilizing both RNA and DNA in plant tissue samples. Our work indicated that total RNA or DNA extracted from virus-infected leaf samples preserved in RNAlater® was suitable for reverse transcription polymerase chain reaction (RT-PCR), PCR, Sanger sequencing, high-throughput sequencing (HTS), and enzyme-linked immunosorbent assay (ELISA)-based diagnostic analyses. We demonstrated the effectiveness of this technology using leaf tissue samples from plants with virus symptoms grown in farmers’ fields in Bangladesh. The results revealed that RNAlater® technology was effective for detection and characterization of viruses from samples collected from remote areas and stored for extended periods. Adoption of this technology by developing countries with limited laboratory facilities could greatly increase their capacity to detect and diagnose viral infections in crop plants using modern analytical techniques.
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Affiliation(s)
- Islam Hamim
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
- *Correspondence: Islam Hamim,
| | - Jon Y. Suzuki
- USDA-ARS, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI, United States
| | - Wayne B. Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Michael J. Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Marisa M. Wall
- USDA-ARS, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI, United States
| | - John S. Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
- John S. Hu,
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Brown LG, Haack AJ, Kennedy DS, Adams KN, Stolarczuk JE, Takezawa MG, Berthier E, Thongpang S, Lim FY, Chaussabel D, Garand M, Theberge AB. At-home blood collection and stabilization in high temperature climates using homeRNA. Front Digit Health 2022; 4:903153. [PMID: 36033636 PMCID: PMC9405416 DOI: 10.3389/fdgth.2022.903153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Expanding whole blood sample collection for transcriptome analysis beyond traditional phlebotomy clinics will open new frontiers for remote immune research and telemedicine. Determining the stability of RNA in blood samples exposed to high ambient temperatures (>30°C) is necessary for deploying home-sampling in settings with elevated temperatures (e.g., studying physiological response to natural disasters that occur in warm locations or in the summer). Recently, we have developed homeRNA, a technology that allows for self-blood sampling and RNA stabilization remotely. homeRNA consists of a lancet-based blood collection device, the Tasso-SST™ which collects up to 0.5 ml of blood from the upper arm, and a custom-built stabilization transfer tube containing RNAlater™. In this study, we investigated the robustness of our homeRNA kit in high temperature settings via two small pilot studies in Doha, Qatar (no. participants = 8), and the Western and South Central USA during the summer of 2021, which included a heatwave of unusually high temperatures in some locations (no. participants = 11). Samples collected from participants in Doha were subjected to rapid external temperature fluctuations from being moved to and from air-conditioned areas and extreme heat environments (up to 41°C external temperature during brief temperature spikes). In the USA pilot study, regions varied in outdoor temperature highs (between 25°C and 43.4°C). All samples that returned a RNA integrity number (RIN) value from the Doha, Qatar group had a RIN ≥7.0, a typical integrity threshold for downstream transcriptomics analysis. RIN values for the Western and South Central USA samples (n = 12 samples) ranged from 6.9–8.7 with 9 out of 12 samples reporting RINs ≥7.0. Overall, our pilot data suggest that homeRNA can be used in some regions that experience elevated temperatures, opening up new geographical frontiers in disseminated transcriptome analysis for applications critical to telemedicine, global health, and expanded clinical research. Further studies, including our ongoing work in Qatar, USA, and Thailand, will continue to test the robustness of homeRNA.
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Affiliation(s)
- Lauren G. Brown
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Amanda J. Haack
- Department of Chemistry, University of Washington, Seattle, WA, United States
- School of Medicine, University of Washington, Seattle, WA, United States
| | - Dakota S. Kennedy
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Karen N. Adams
- Institute of Translational Health Sciences, School of Medicine, University of Washington, Seattle, WA, United States
| | | | - Meg G. Takezawa
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Erwin Berthier
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Sanitta Thongpang
- Department of Chemistry, University of Washington, Seattle, WA, United States
- Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakorn Pathom, Thailand
| | - Fang Yun Lim
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Damien Chaussabel
- Research Branch, Sidra Medicine, Doha, Qatar
- Computer Sciences Department, The Jackson Laboratory, Farmington, CT, United States
- Correspondence: Ashleigh B. Theberge Mathieu Garand Damien Chaussabel
| | - Mathieu Garand
- Research Branch, Sidra Medicine, Doha, Qatar
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States
- Correspondence: Ashleigh B. Theberge Mathieu Garand Damien Chaussabel
| | - Ashleigh B. Theberge
- Department of Chemistry, University of Washington, Seattle, WA, United States
- Department of Urology, School of Medicine, University of Washington, Seattle, WA, United States
- Correspondence: Ashleigh B. Theberge Mathieu Garand Damien Chaussabel
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20
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Yin Q, Qiao R, Xu T, Dai L, Han B, Gu W, Yang R. The influence of blood sample processing on blood-based DNA methylation signatures. Clin Biochem 2022; 115:116-125. [PMID: 35787405 DOI: 10.1016/j.clinbiochem.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/07/2022] [Accepted: 06/29/2022] [Indexed: 11/03/2022]
Abstract
Stability is crucial for the clinical applicable biomarker such as DNA methylation profiles. However, the influence of various blood processing on the DNA methylation signatures have been barely studied. Here, we systematically evaluated the impact of temporary storage and frozen and thaw on the levels of DNA methylation. The methylation intensities of 13 CpG loci from 53 individuals (42 healthy participants and 11 lung cancer patients) whose blood samples were processed by up to 14 various protocols were quantitatively determined by the mass spectrometry, obtaining more than 8,000 quantitative data. We disclosed a trend of accumulatively increased DNA methylation along with time when the blood from healthy people were stored for up to 96 hours at room temperature (RT), whereas the storage at 4℃ had much weaker effects or no impact. On the contrary, the methylation patterns in the blood of lung cancer patients were more stable at both RT and 4℃ even for 96 hours. Multiple cycles of frozen and thaw could result in demethylation, but was more significant to the blood than to the extracted DNA. Our study indicated that the blood processing in vitro could influence the DNA methylation signatures and introduce unexpected biases.
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Affiliation(s)
- Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.
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21
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Elliott CI, Stotesbury TE, Shafer ABA. Using total RNA quality metrics for time since deposition estimates in degrading bloodstains. J Forensic Sci 2022; 67:1776-1785. [PMID: 35665927 DOI: 10.1111/1556-4029.15072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 12/23/2022]
Abstract
The physicochemical changes occurring in biomolecules in degrading bloodstains can be used to approximate the time since deposition (TSD) of bloodstains. This would provide forensic scientists with critical information regarding the timeline of the events involving bloodshed. Our study aims to quantify the timewise degradation trends and temperature dependence found in total RNA from bloodstains without the use of amplification, expanding the scope of the RNA TSD research which has traditionally targeted mRNA and miRNA. Bovine blood with ACD-A anticoagulant was deposited and stored in plastic microcentrifuge tubes at 21 or 4°C and tested over different timepoints spanning 1 week. Total RNA was extracted from each sample and analyzed using automated high sensitivity gel electrophoresis. Nine RNA metrics were visually assessed and quantified using linear and mixed models. The RNA Integrity Number equivalent (RINe) and DV200 were not influenced by the addition of anticoagulant and demonstrated strong negative trends over time. The RINe model fit was high (R2 = 0.60), and while including the biological replicate as a random effect increased the fit for all RNA metrics, no significant differences were found between biological replicates stored at the same temperature for the RINe and DV200. This suggests that these standardized metrics can be directly compared between scenarios and individuals, with DV200 having an inflection point at approximately 28 h. This study provides a novel approach for blood TSD research, revealing metrics that are not affected by inter-individual variation, and improving our understanding of the rapid RNA degradation occurring in bloodstains.
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Affiliation(s)
- Colin I Elliott
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada.,Applied Bioscience Graduate Program, Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
| | - Theresa E Stotesbury
- Faculty of Science, Forensic Science, Ontario Tech University, Oshawa, Ontario, Canada
| | - Aaron B A Shafer
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada.,Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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22
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Cameron JM, Rinaldi C, Rutherford SH, Sala A, G Theakstone A, Baker MJ. Clinical Spectroscopy: Lost in Translation? APPLIED SPECTROSCOPY 2022; 76:393-415. [PMID: 34041957 DOI: 10.1177/00037028211021846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This Focal Point Review paper discusses the developments of biomedical Raman and infrared spectroscopy, and the recent strive towards these technologies being regarded as reliable clinical tools. The promise of vibrational spectroscopy in the field of biomedical science, alongside the development of computational methods for spectral analysis, has driven a plethora of proof-of-concept studies which convey the potential of various spectroscopic approaches. Here we report a brief review of the literature published over the past few decades, with a focus on the current technical, clinical, and economic barriers to translation, namely the limitations of many of the early studies, and the lack of understanding of clinical pathways, health technology assessments, regulatory approval, clinical feasibility, and funding applications. The field of biomedical vibrational spectroscopy must acknowledge and overcome these hurdles in order to achieve clinical efficacy. Current prospects have been overviewed with comment on the advised future direction of spectroscopic technologies, with the aspiration that many of these innovative approaches can ultimately reach the frontier of medical diagnostics and many clinical applications.
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Affiliation(s)
| | - Christopher Rinaldi
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
| | - Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
| | - Alexandra Sala
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
| | - Ashton G Theakstone
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
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23
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Martire S, Valentino P, Marnetto F, Mirabile L, Capobianco M, Bertolotto A. The impact of pre-freezing storage time and temperature on gene expression of blood collected in EDTA tubes. Mol Biol Rep 2022; 49:4709-4718. [PMID: 35279776 PMCID: PMC9262796 DOI: 10.1007/s11033-022-07320-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/02/2022] [Indexed: 12/03/2022]
Abstract
Background Blood is a common source of RNA for gene expression studies. However, it is known to be vulnerable to pre-analytical variables. Although RNA stabilization systems have been shown to reduce such influence, traditional EDTA tubes are still widely used since they are less expensive and enable to study specific leukocyte populations. This study aimed to assess the influence of storage time and temperature between blood sampling and handling on RNA from peripheral blood mononuclear cells (PBMCs). Methods and results Nine blood samples were collected in EDTA tubes from 10 healthy donors. One tube from each donor was immediately processed for PBMC isolation, while the others were first incubated at either 4 degrees Celsius (°C) or room temperature for 2, 4, 6 and 24 h. RNA yield and quality and the expression level of fourt housekeeping (B2M, CASC3, GAPDH, HPRT1) and 8 target genes (CD14, CD19, CD20, IL10, MxA, TNF, TNFAIP3, NR4A2) were compared between samples. RNA yield, quality and integrity did not vary significantly with time and temperature. B2M was the most stable housekeeping gene, while the others were increasingly influenced by storing time, especially at 4 °C. Even when normalized to B2M, the expression level of some target genes, particularly TNFAIP3 and NR4A2, was highly affected by delays in blood processing at either temperature, already from 2 h. Conclusion Pre-analytical processing has a great impact on transcript expression from blood collected in EDTA tubes, especially on genes related to inflammation. Standardized procedure of blood handling are needed to obtain reliable results. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07320-5.
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Affiliation(s)
- Serena Martire
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy.
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10100, Turin, Italy.
| | - Paola Valentino
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10100, Turin, Italy
| | - Fabiana Marnetto
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10100, Turin, Italy
| | - Luca Mirabile
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
| | - Marco Capobianco
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- SCDO Neurologia and CRESM, University Hospital AOU San Luigi Gonzaga, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Antonio Bertolotto
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- Koelliker Hospital, 10100, Turin, Italy
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24
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LncRNA Biomarkers of Inflammation and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:121-145. [PMID: 35220568 DOI: 10.1007/978-3-030-92034-0_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are promising candidates as biomarkers of inflammation and cancer. LncRNAs have several properties that make them well-suited as molecular markers of disease: (1) many lncRNAs are expressed in a tissue-specific manner, (2) distinct lncRNAs are upregulated based on different inflammatory or oncogenic stimuli, (3) lncRNAs released from cells are packaged and protected in extracellular vesicles, and (4) circulating lncRNAs in the blood are detectable using various RNA sequencing approaches. Here we focus on the potential for lncRNA biomarkers to detect inflammation and cancer, highlighting key biological, technological, and analytical considerations that will help advance the development of lncRNA-based liquid biopsies.
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25
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Abstract
Epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are increasingly targeted in studies of natural populations. Here, I review some of the insights gained from this research, examine some of the methods currently in use and discuss some of the challenges that researchers working on natural populations are likely to face when probing epigenetic mechanisms. While studies supporting the involvement of epigenetic mechanisms in generating phenotypic variation in natural populations are amassing, many of these studies are currently correlative in nature. Thus, while empirical data point to widespread contributions of epigenetic mechanisms in generating phenotypic variation, there are still concerns as to whether epigenetic variation is instead ultimately controlled by genetic variation. Disentangling these two sources of variation will be a key to resolving the debate about the importance of epigenetic mechanisms, and studies on natural populations that partition the relative contribution of genetic and epigenetic factors to phenotypic variation can play an important role in this debate.
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Affiliation(s)
- Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden.,Centre for Biodiversity Dynamics, Norwegian University for Science and Technology, Trondheim, Norway
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26
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Lin M, Eberlin LS, Seeley EH. Reduced Hemoglobin Signal and Improved Detection of Endogenous Proteins in Blood-Rich Tissues for MALDI Mass Spectrometry Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:296-303. [PMID: 35061381 PMCID: PMC9041275 DOI: 10.1021/jasms.1c00300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Mass spectrometry imaging provides a powerful approach for the direct analysis and spatial visualization of molecules in tissue sections. Using matrix-assisted laser desorption/ionization mass spectrometry, intact protein imaging has been widely investigated for biomarker analysis and diagnosis in a variety of tissue types and diseases. However, blood-rich or highly vascular tissues present a challenge in molecular imaging due to the high ionization efficiency of hemoglobin, which leads to ion suppression of endogenous proteins. Here, we describe a protocol to selectively reduce hemoglobin signal in blood-rich tissues that can easily be integrated into mass spectrometry imaging workflows.
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Affiliation(s)
- Monica Lin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Livia S. Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
- Department of Surgery, Baylor College of Medicine, Houston, TX 77030
- to whom correspondence may be addressed: ,
| | - Erin H. Seeley
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
- to whom correspondence may be addressed: ,
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27
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Zhang Z, Lee MK, Perreard L, Kelsey KT, Christensen BC, Salas LA. Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem bisulfite and oxidative bisulfite Illumina microarrays. Epigenomics 2022; 14:139-152. [PMID: 35029129 PMCID: PMC8914583 DOI: 10.2217/epi-2021-0490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Aim: Tandem bisulfite (BS) and oxidative bisulfite (oxBS) conversion on DNA followed by hybridization to Infinium HumanMethylation BeadChips allows nucleotide resolution of 5-hydroxymethylcytosine genome-wide. Here, the authors compared data quality acquired from BS-treated and oxBS-treated samples. Materials & methods: Raw BeadArray data from 417 pairs of samples across 12 independent datasets were included in the study. Probe call rates were compared between paired BS and oxBS treatments controlling for technical variables. Results: oxBS-treated samples had a significantly lower call rate. Among technical variables, DNA-specific extraction kits performed better with higher call rates after oxBS conversion. Conclusion: The authors emphasize the importance of quality control during oxBS conversion to minimize information loss and recommend using a DNA-specific extraction kit for DNA extraction and an oxBSQC package for data preprocessing.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Laurent Perreard
- Department of Molecular & Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Karl T Kelsey
- Department of Epidemiology, Department of Pathology & Laboratory Medicine, Brown University School of Public Health, Providence, 02912 RI, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA,Department of Molecular & Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA,Department of Molecular & Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA,Author for correspondence: Tel.: 603 646 5496;
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Manirakiza G, Kassaza K, Taremwa IM, Bazira J, Byarugaba F. Molecular identification and anti-malarial drug resistance profile of Plasmodium falciparum from patients attending Kisoro Hospital, southwestern Uganda. Malar J 2022; 21:21. [PMID: 35033082 PMCID: PMC8761270 DOI: 10.1186/s12936-021-04023-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022] Open
Abstract
Background The evolution of malaria infection has necessitated the development of highly sensitive diagnostic assays, as well as the use of dried blood spots (DBS) as a potential source of deoxyribonucleic acid (DNA) yield for polymerase chain reaction (PCR) assays. This study identified the different Plasmodium species in malaria-positive patients, and the anti-malarial drug resistance profile for Plasmodium falciparum using DBS samples collected from patients attending Kisoro Hospital in Kisoro district, Southwestern Uganda. Methods The blood samples were prospectively collected from patients diagnosed with malaria to make DBS, which were then used to extract DNA for real-time PCR and high-resolution melting (HRM) analysis. Plasmodium species were identified by comparing the control and test samples using HRM-PCR derivative curves. Plasmodium falciparum chloroquine (CQ) resistance transporter (pfcrt) and kelch13 to screen the samples for anti-malarial resistance markers. The HRM-PCR derivative curve was used to present a summary distribution of the different Plasmodium species as well as the anti-malarial drug profile. Results Of the 152 participants sampled, 98 (64.5%) were females. The average age of the participants was 34.9 years (range: 2 months–81 years). There were 134 samples that showed PCR amplification, confirming the species as Plasmodium. Plasmodium falciparum (N = 122), Plasmodium malariae (N = 6), Plasmodium ovale (N = 4), and Plasmodium vivax (N = 2) were the various Plasmodium species and their proportions. The results showed that 87 (71.3%) of the samples were sensitive strains/wild type (CVMNK), 4 (3.3%) were resistant haplotypes (SVMNT), and 31 (25.4%) were resistant haplotypes (CVIET). Kelch13 C580Y mutation was not detected. Conclusion The community served by Kisoro hospital has a high Plasmodium species burden, according to this study. Plasmodium falciparum was the dominant species, and it has shown that resistance to chloroquine is decreasing in the region. Based on this, molecular identification of Plasmodium species is critical for better clinical management. Besides, DBS is an appropriate medium for DNA preservation and storage for future epidemiological studies.
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Affiliation(s)
- Godfrey Manirakiza
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda.
| | - Kennedy Kassaza
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Ivan Mugisha Taremwa
- Institute of Allied Health Sciences, Clarke International University, Kampala, Uganda
| | - Joel Bazira
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Fredrick Byarugaba
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
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29
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Romanyuk SA, Popov OS, Sushentseva NN, Apalko SV, Polkovnikova IA, Shcherbak SG. Optimization of RNA storage in a biobank, as well as methods for manual and automated isolation of RNA from whole blood and leukocyte fraction. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2021-3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Aim. To optimize the technique for the isolation and storage of ribonucleic acid (RNA) from whole blood and leukocyte fraction.Materials and methods. Comparison of isolation quality was carried out for RNA samples obtained from 228 leukocyte samples and 198 whole blood samples. Isolation was performed from fresh and frozen samples using ExtractRNA™ reagent and a MagNA Pure Compact automated system. Various methods of removing erythrocytes (centrifugation and treatment with hemolytic agents from two manufacturers) were tested, as well as freezing with and without preservatives for subsequent RNA isolation.Results. Twenty-one combinations of conditions were tested. The highest quality RNA was isolated by manual extraction using the ExtractRNA™ reagent from a fresh leukocyte fraction, purified by the Amplisens hemolytic agent (successful extraction — 94%, median RIN=8,4); frozen in IntactRNA™, purified by leukocyte fraction centrifugation (successful extraction — 100%, median RIN=8); frozen in ExtractRNA™, purified by leukocyte fraction centrifugation (successful extraction — 100%, median RIN=9,3).Conclusion. RNA can be isolated from frozen blood fractions, which is not inferior in quality to that isolated from fresh samples. Thus, it is not necessary to isolate RNA immediately after the receipt of biological material.
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30
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Binetti L, Simpson F, Alwis LSM. Evaluation of Viscosity Dependence of the Critical Meniscus Height with Optical Fiber Sensors. SENSORS 2021; 21:s21238130. [PMID: 34884134 PMCID: PMC8662447 DOI: 10.3390/s21238130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 12/03/2022]
Abstract
Conventional means of data extraction using optical fiber interrogators are not adequate for fast-paced detection of a target parameter. In this instance, the relationship between the critical meniscus heights (CMH) of several liquids to the extraction speed of a rod submerged in them, have been analyzed. A limitation of a previous interrogator used for the purpose had been light absorption by the liquid due to the used bandwidth of the readily-available light source, i.e., C-band. The newly proposed technique addresses this limitation by utilizing a broadband light source instead, with a Si-photodetector and an Arduino. In addition, the Arduino is capable of extracting data at a relatively faster rate with respect to the conventional optical interrogator. The use of a different operational wavelength (850 nm instead of 1550 nm) increased the r2 and the sensitivity of the sensor. The new setup can measure surface chemistry properties, with the advantage of being comparatively cheaper than the conventionally available interrogator units, thereby providing a suitable alternative to conventional measurement techniques of liquid surface properties, while reducing material waste, i.e., in terms of the required volume for detection of a target parameter, through the use of optical fiber.
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31
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Paul P, Rajput S, Joshi P, Naithani M, Chowdhury N, Rao S, Pai MO. Comparison of Fluorometric and UV Spectrophotometric Findings for DNA Isolated From Formalin-Fixed Paraffin-Embedded Blocks, Fine Needle Aspiration Cytology Smears, and Blood. Cureus 2021; 13:e19583. [PMID: 34926054 PMCID: PMC8672151 DOI: 10.7759/cureus.19583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2021] [Indexed: 12/04/2022] Open
Abstract
Introduction: Fine needle aspiration cytology (FNAC) smear may serve as a convenient sample for DNA extraction for molecular pathology in addition to more commonly used formalin-fixed paraffin-embedded (FFPE) sections. DNA quantification done by fluorometer is more accurate than UV vis spectrophotometer regardless of the source. This study was conducted to compare DNA yield and quality from cytology smears, FFPE sections and peripheral blood using both fluorometer and spectrophotometer. Further, introspection was made to check for the adequacy of DNA extracted from cytology smears with respect to DNA extracted from core biopsies. Method: DNA was extracted from 10 fresh peripheral blood samples, core biopsies and FNAC smears. The DNA was quantified using a fluorimeter and UV vis spectrophotometer in all cases. Results: Statistically significant difference was seen between the data obtained from UV vis spectrophotometry and flourometry. The quantity of DNA extracted from FNAC smears was higher than that of core biopsy as per fluorometry data (mean DNA of core biopsy = 1.9ng/µl, of FNAC = 3.3ng/µl). Conclusion: DNA estimation by fluorometry is more accurate and precise than spectrophotometry in FFPE, FNAC and whole blood samples. DNA yield from FNAC slides is comparable to that from core biopsies.
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Lager M, Wilhelmsson P, Matussek A, Lindgren PE, Henningsson AJ. Molecular Detection of Borrelia Bacteria in Cerebrospinal Fluid-Optimisation of Pre-Analytical Sample Handling for Increased Analytical Sensitivity. Diagnostics (Basel) 2021; 11:diagnostics11112088. [PMID: 34829435 PMCID: PMC8623531 DOI: 10.3390/diagnostics11112088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022] Open
Abstract
The main tools for clinical diagnostics of Lyme neuroborreliosis (LNB) are based on serology, i.e., detection of antibodies in cerebrospinal fluid (CSF). In some cases, PCR may be used as a supplement, e.g., on CSF from patients with early LNB. Standardisation of the molecular methods and systematic evaluation of the pre-analytical handling is lacking. To increase the analytical sensitivity for detection of Borrelia bacteria in CSF by PCR targeting the 16S rRNA gene, parameters were systematically evaluated on CSF samples spiked with a known amount of cultured Borrelia bacteria. The results showed that the parameters such as centrifugation time and speed, the use of complementary DNA as a template (in combination with primers and a probe aiming at target gene 16S rRNA), and the absence of inhibitors (e.g., erythrocytes) had the highest impact on the analytical sensitivity. Based on these results, a protocol for optimised handling of CSF samples before molecular analysis was proposed. However, no clinical evaluation of the proposed protocol has been done so far, and further investigations of the diagnostic sensitivity need to be performed on well-characterised clinical samples from patients with LNB.
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Affiliation(s)
- Malin Lager
- Division of Clinical Microbiology, Laboratory Medicine (Region Jönköping County, 553 05 Jönköping, Sweden), Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden; (P.W.); (A.M.); (P.-E.L.); (A.J.H.)
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Correspondence: ; Tel.: +46-(0)10-2425238
| | - Peter Wilhelmsson
- Division of Clinical Microbiology, Laboratory Medicine (Region Jönköping County, 553 05 Jönköping, Sweden), Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden; (P.W.); (A.M.); (P.-E.L.); (A.J.H.)
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Andreas Matussek
- Division of Clinical Microbiology, Laboratory Medicine (Region Jönköping County, 553 05 Jönköping, Sweden), Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden; (P.W.); (A.M.); (P.-E.L.); (A.J.H.)
- Division of Laboratory Medicine, Oslo University Hospital, 0450 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
| | - Per-Eric Lindgren
- Division of Clinical Microbiology, Laboratory Medicine (Region Jönköping County, 553 05 Jönköping, Sweden), Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden; (P.W.); (A.M.); (P.-E.L.); (A.J.H.)
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Anna J. Henningsson
- Division of Clinical Microbiology, Laboratory Medicine (Region Jönköping County, 553 05 Jönköping, Sweden), Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden; (P.W.); (A.M.); (P.-E.L.); (A.J.H.)
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Division of Clinical Microbiology, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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How long does the mRNA remains stable in untreated whole bovine blood? Mol Biol Rep 2021; 49:789-795. [PMID: 34655019 DOI: 10.1007/s11033-021-06808-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND High quality and quantity of messenger RNA (mRNA) are required for accuracy of gene expression studies and other RNA-based downstream applications. Since RNA is considered a labile macromolecular prone to degradation, which may result in falsely altered gene expression patterns, several commercial stabilizing reagents have been developed aiming to keep RNA stable for long period. However, for studies involving large number of experimental samples, the high costs related to these specific reagents may constitute a barrier. METHODS AND RESULTS In this context the present study was designed aiming to evaluate the stability of mRNA in whole bovine blood collected in EDTA tubes during storage at common fridge (4 °C). Whole blood samples were collected from six Holstein calves and submitted to RNA extraction in each different interval: immediately after blood sampling (< 2 h), at 1-day post-sampling (dps), 2 dps, 3 dps, 7 dps and 14dps intervals. RNA integrity and purity were evaluated, and RT-qPCR assays were run using seven different genes (B2M, ACTB, PPIA, GAPDH, YWHAZ, CD4 and IFN-γ) aiming to evaluate the presence of altered gene transcription during storage. All extracted RNA samples presented high purity, while optimal integrity and unaltered gene expression were observed in whole experimental group up to 3 days of storage. CONCLUSION Bovine blood RNA remained stable in K3EDTA tubes for 3 days stored at common fridge and can be successfully and accurately used for gene expression studies.
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Idiopathic early ovarian aging: is there a relation with premenopausal accelerated biological aging in young women with diminished response to ART? J Assist Reprod Genet 2021; 38:3027-3038. [PMID: 34599460 DOI: 10.1007/s10815-021-02326-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To evaluate whether young women with idiopathic early ovarian aging, as defined by producing fewer oocytes than expected for a given age over multiple in vitro fertilization (IVF) cycles, have changes in telomere length and epigenetic age indicating accelerated biological aging (i.e., increased risk of morbidity and mortality). METHODS A prospective cohort study was conducted at two Danish public fertility clinics. A total of 55 young women (≤ 37 years) with at least two IVF cycles with ≤ 5 harvested oocytes despite sufficient stimulation with follicle-stimulating hormone (FSH) were included in the early ovarian aging group. As controls, 52 young women (≤ 37 years) with normal ovarian function, defined by at least eight harvested oocytes, were included. Relative telomere length (rTL) and epigenetic age acceleration (AgeAccel) were measured in white blood cells as markers of premenopausal accelerated biological aging. RESULTS rTL was comparable with a mean of 0.46 (± SD 0.12) in the early ovarian aging group and 0.47 (0.14) in the normal ovarian aging group. The AgeAccel of the early ovarian aging group was, insignificantly, 0.5 years older, but this difference disappeared when adjusting for chronological age. Sub-analysis using Anti-Müllerian hormone (AMH) as selection criterion for the two groups did not change the results. CONCLUSION We did not find any indications of accelerated aging in whole blood from young women with idiopathic early ovarian aging. Further investigations in a similar cohort of premenopausal women or other tissues are needed to fully elucidate the potential relationship between premenopausal accelerated biological aging and early ovarian aging.
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Sahoo S, Mandal S, Das P, Bhattacharya S, Chandy M. An analysis of the standard curve parameters of cytomegalovirus, BK virus and hepatitis B virus quantitative polymerase chain reaction from a clinical virology laboratory in eastern India. Indian J Med Microbiol 2021; 40:81-85. [PMID: 34602291 DOI: 10.1016/j.ijmmb.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 11/05/2022]
Abstract
PURPOSE Quantitative real-time polymerase chain reactions (qPCRs) are important for accurate detection of nucleic acid target including that for viral load determination. Assessment of the quality of a PCR run is essential for quality control, diagnostics and research. In order to reduce subjectivity qPCR standard curves are accompanied with parametric values for slope, Y- intercept, correlation coefficient (R2) and PCR efficiency. In this study the performance of three qPCR assays-cytomegalovirus, hepatitis B virus and BK virus-with respect to standard curve parameters-slope, Y intercept, R2 and efficiency were examined. METHODS Using ideal values (Slope (minus 3.32); Y intercept = the number of PCR cycles; R2 = 1 and efficiency = 100%) we estimated the intra-assay variability (range) and deviation from ideal parameters (Δ). We also calculated the standard deviation (SD) and coefficient of variation (CV) for each of these parameters. We have evaluated the quality of each of the three viral load assays (CMV, HBV, BKV) using these statistical approach. RESULTS We found lab developed tests (CMV) to have least deviation from ideal Y intercept (limit of detection); however, commercial kit based assays had better linearity (scatter plot correlation between amplification factor and PCR efficiency). Using a scatter plot for the three assays we found the correlation with calculated amplification factor and PCR efficiency was most linear in case of BKV (0.9974), closely followed by the HBV assay (R2 = 0.9968). Although the CMV quantitative standards were least linear (0.868), the CV (coefficient of variation) was also the least in case of the CMV assay. CONCLUSION The study highlights an objective way of assessing qPCR assay quality and demonstrates a method to compare assays, validate tests and perform quality control.
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Affiliation(s)
- Sunanda Sahoo
- Department of Microbiology, Tata Medical Center, Kolkata, India
| | - Sudipto Mandal
- Department of Microbiology, Tata Medical Center, Kolkata, India
| | - Parijat Das
- Department of Microbiology, Tata Medical Center, Kolkata, India
| | | | - Mammen Chandy
- Department of Clinical Hematology, Tata Medical Center, Kolkata, India
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Le Masters T, Johnson S, Jeraldo PR, Greenwood-Quaintance KE, Cunningham SA, Abdel MP, Chia N, Patel R. Comparative Transcriptomic Analysis of Staphylococcus aureus Associated with Periprosthetic Joint Infection under in Vivo and in Vitro Conditions. J Mol Diagn 2021; 23:986-999. [PMID: 34098085 DOI: 10.1016/j.jmoldx.2021.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/25/2021] [Accepted: 05/06/2021] [Indexed: 11/15/2022] Open
Abstract
Transcriptomic analysis can provide insight as to how Staphylococcus aureus adapts to the environmental niche of periprosthetic joint infection (PJI), a challenging clinical infection. Here, in vivo RNA expression of eight S. aureus PJIs was compared with expression of the corresponding isolates in planktonic culture using a total RNA-sequencing approach. Expression varied among isolates, with a common trend showing increased expression of several ica-independent biofilm formation genes, including sdr, fnb, ebpS, and aaa; genes encoding enzymes and toxins, including coa, nuc, hlb, and hlgA/B/C; and genes facilitating acquisition of iron via the iron-binding molecule siderophore B (snb) and heme consumption protein (isd) pathways in PJI. Several antimicrobial resistance determinants were detected; although their presence correlated with phenotypic susceptibility of the associated isolates, no difference in expression between in vivo and in vitro conditions was identified.
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Affiliation(s)
- Thao Le Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephen Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Patricio R Jeraldo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Scott A Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota.
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Nasser F, Cruz-Garcia L, O'Brien G, Badie C. Role of blood derived cell fractions, temperature and sample transport on gene expression-based biological dosimetry. Int J Radiat Biol 2021; 97:675-686. [PMID: 33826469 DOI: 10.1080/09553002.2021.1906464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE For triage purposes following a nuclear accident or a terrorist event, gene expression biomarkers in blood have been demonstrated to be good bioindicators of ionizing radiation (IR) exposure and can be used to assess the dose received by exposed individuals. Many IR-sensitive genes are regulated by the DNA damage response pathway, and modulators of this pathway could potentially affect their expression level and therefore alter accurate dose estimations. In the present study, we addressed the potential influence of temperature, sample transport conditions and the blood cell fraction analyzed on the transcriptional response of the following radiation-responsive genes: FDXR, CCNG1, MDM2, PHPT1, APOBEC3H, DDB2, SESN1, P21, PUMA, and GADD45. MATERIALS AND METHODS Whole blood from healthy donors was exposed to a 2 Gy X-ray dose with a dose rate of 0.5 Gy/min (output 13 mA, 250 kV peak, 0.2 mA) and incubated for 24 h at either 37, 22, or 4 °C. For mimicking the effect of transport conditions at different temperatures, samples incubated at 37 °C for 24 h were kept at 37, 22 or 4 °C for another 24 h. Comparisons of biomarker responses to IR between white blood cells (WBCs), peripheral blood mononuclear cells (PBMCs) and whole blood were carried out after a 2 Gy X-ray exposure and incubation at 37 °C for 24 hours. RESULTS Hypothermic conditions (22 or 4 °C) following irradiation drastically inhibited transcriptional responses to IR exposure. However, sample shipment at different temperatures did not affect gene expression level except for SESN1. The transcriptional response to IR of specific genes depended on the cell fraction used, apart from FDXR, CCNG1, and SESN1. CONCLUSION In conclusion, temperature during the incubation period and cell fraction but not the storing conditions during transport can influence the transcriptional response of specific genes. However, FDXR and CCNG1 showed a consistent response under all the different conditions tested demonstrating their reliability as individual biological dosimetry biomarkers.
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Affiliation(s)
- Farah Nasser
- Radiation Effects Department, Cancer Mechanisms and Biomarkers Group, Centre for Radiation, Chemical & Environmental Hazards, Public Health England, Chilton, Oxfordshire, United Kingdom
| | - Lourdes Cruz-Garcia
- Radiation Effects Department, Cancer Mechanisms and Biomarkers Group, Centre for Radiation, Chemical & Environmental Hazards, Public Health England, Chilton, Oxfordshire, United Kingdom
| | - Grainne O'Brien
- Radiation Effects Department, Cancer Mechanisms and Biomarkers Group, Centre for Radiation, Chemical & Environmental Hazards, Public Health England, Chilton, Oxfordshire, United Kingdom
| | - Christophe Badie
- Radiation Effects Department, Cancer Mechanisms and Biomarkers Group, Centre for Radiation, Chemical & Environmental Hazards, Public Health England, Chilton, Oxfordshire, United Kingdom
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Andrade FG, Feliciano SVM, Sardou-Cezar I, Brisson GD, Dos Santos-Bueno FV, Vianna DT, Marques LVC, Terra-Granado E, Zalcberg I, Santos MDO, Costa JT, Noronha EP, Thuler LCS, Wiemels JL, Pombo-de-Oliveira MS. Pediatric Acute Promyelocytic Leukemia: Epidemiology, Molecular Features, and Importance of GST-Theta 1 in Chemotherapy Response and Outcome. Front Oncol 2021; 11:642744. [PMID: 33816294 PMCID: PMC8017304 DOI: 10.3389/fonc.2021.642744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/08/2021] [Indexed: 11/23/2022] Open
Abstract
Previous studies have suggested a variation in the incidence of acute promyelocytic leukemia (APL) among the geographic regions with relatively higher percentages in the Latin American population. We aimed to explore the population burden of pediatric APL, gathering information from the population-based cancer registry (PBCR) and the diagnosis of APL obtained through incident cases from a hospital-based cohort. The homozygous deletion in glutathione S-transferases (GSTs) leads to a loss of enzyme detoxification activity, possibly affecting the treatment response. Mutations in the RAS pathway genes are also considered to be a key component of the disease both in the pathogenesis and in the outcomes. We have assessed mutations in a RAS–MAP kinase pathway (FLT3, PTPN11, and K-/NRAS) and GST variant predisposition risk in the outcome. Out of the 805 children and adolescents with acute myeloid leukemia (AML) who are registered in the PBCR, 35 (4.3%) were APL cases. The age-adjusted incidence rate (AAIR) was 0.03 per 100,000 person-years. One-hundred and sixty-three patients with APL were studied out of 931 AML cases (17.5%) from a hospital-based cohort. Mutations in FLT3, KRAS, and NRAS accounted for 52.1% of the cases. Patients with APL presented a 5-year probability of the overall survival (OS) of 67.3 ± 5.8%. A GST-theta 1 (GSTT1) null genotype conferred adverse prognosis, with an estimated hazard ratio of 2.8, 95% confidence interval (CI) 1.2–6.9. We speculate that the GSTT1 polymorphism is associated with therapeutics and would allow better OS of patients with APL with a GSTT1 null genotype.
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Affiliation(s)
- Francianne G Andrade
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Suellen V M Feliciano
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Ingrid Sardou-Cezar
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Gisele D Brisson
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Filipe V Dos Santos-Bueno
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Danielle T Vianna
- Laboratory of Molecular Biology, Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Luísa V C Marques
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Eugênia Terra-Granado
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Ilana Zalcberg
- Laboratory of Molecular Biology, Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Marceli de O Santos
- Surveillance and Prevention, Instituto Nacional de Cancer, Rio de Janeiro, Brazil
| | - Juliana T Costa
- Department of Pediatric Hematology-Oncology, Hospital Martagão Gesteira, Salvador, Brazil
| | - Elda P Noronha
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Luiz C S Thuler
- Clinical Research Department, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
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Borsky P, Chmelarova M, Fiala Z, Hamakova K, Palicka V, Krejsek J, Andrys C, Kremlacek J, Rehacek V, Beranek M, Malkova A, Svadlakova T, Holmannova D, Borska L. Aging in psoriasis vulgaris: female patients are epigenetically older than healthy controls. Immun Ageing 2021; 18:10. [PMID: 33658053 PMCID: PMC7927262 DOI: 10.1186/s12979-021-00220-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/10/2021] [Indexed: 12/26/2022]
Abstract
Background Psoriasis vulgaris is a skin autoimmune disease. Psoriatic patients have significantly lowered life expectancy and suffer from various comorbidities. The main goal of the study was to determine whether psoriatic patients experience accelerated aging. As accelerated aging might be the reason for the higher prevalence of comorbidities at lower chronological ages, we also wanted to investigate the relationship between aging and selected parameters of frequent psoriatic comorbidities - endocan, vascular endothelial growth factor and interleukin-17. Samples were obtained from 28 patients and 42 healthy controls. Epigenetic age measurement was based on the Horvath clock. The levels of endocan, vascular endothelial growth factor and interleukin-17 were analyzed using standardized ELISA methods. Results The difference between the epigenetic age and the chronological age of each individual subject did not increase with the increasing chronological age of patients. We cannot conclude that psoriasis causes accelerated aging. However, the epigenetic and chronological age difference was significantly higher in female patients than in female controls, and the difference was correlated with endocan (r = 0.867, p = 0.0012) and vascular endothelial growth factor (r = 0.633, p = 0.0365) only in female patients. Conclusions The findings suggest a possible presence of pathophysiological processes that occur only in female psoriatic patients. These processes make psoriatic females biologically older and might lead to an increased risk of comorbidity occurrence. This study also supports the idea that autoimmune diseases cause accelerated aging, which should be further explored in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12979-021-00220-5.
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Affiliation(s)
- Pavel Borsky
- Institute of Preventive Medicine, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 50038, Hradec Kralove, Czech Republic.
| | - Marcela Chmelarova
- Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Zdenek Fiala
- Institute of Preventive Medicine, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 50038, Hradec Kralove, Czech Republic
| | - Kvetoslava Hamakova
- Clinic of Dermatology and Venereology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Vladimir Palicka
- Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Jan Krejsek
- Institute of Clinical Immunology and Allergology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Ctirad Andrys
- Institute of Clinical Immunology and Allergology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Jan Kremlacek
- Institute of Pathological Physiology, Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Vit Rehacek
- Transfusion Center, University Hospital, 500 03, Hradec Kralove, Czech Republic
| | - Martin Beranek
- Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Andrea Malkova
- Institute of Preventive Medicine, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 50038, Hradec Kralove, Czech Republic
| | - Tereza Svadlakova
- Institute of Preventive Medicine, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 50038, Hradec Kralove, Czech Republic.,Institute of Clinical Immunology and Allergology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Drahomira Holmannova
- Institute of Preventive Medicine, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 50038, Hradec Kralove, Czech Republic
| | - Lenka Borska
- Institute of Pathological Physiology, Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
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Brenier-Pinchart MP, Varlet-Marie E, Robert-Gangneux F, Filisetti D, Guitard J, Sterkers Y, Yera H, Pelloux H, Bastien P. Impact of pre-analytic step duration on molecular diagnosis of toxoplasmosis for five types of biological samples. PLoS One 2021; 16:e0246802. [PMID: 33596222 PMCID: PMC7888589 DOI: 10.1371/journal.pone.0246802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/26/2021] [Indexed: 11/18/2022] Open
Abstract
Introduction Toxoplasma-PCR is essential to diagnose ocular, cerebral, disseminated and congenital toxoplasmosis. This multicenter study evaluated the impact of sample storage duration at +4°C on PCR assay performances in order to propose guidelines for the storage of samples during shipment or/and before PCR. Materials and methods Five matrices, amniotic (AF), cerebrospinal (CSF), and bronchoalveolar lavage fluids (BALF), whole blood (WB) and buffy coat (BC), were artificially spiked with different amounts of Toxoplasma gondii (20, 100, 500 tachyzoites per mL of sample) or with previously infected THP1 cells. DNA extractions were performed at day 0 and after 2, 4 and 7 days of storage at +4°C. Each extract was amplified at least twice by real-time PCR. Results A total of 252 spiked samples was studied. No increase of crossing point was observed and all samples were positive for AF, BALF, BC and infected THP1-spiked WB after up to 7 days at 4°C. For CSF spiked with 20 parasites/mL, only 50% of PCR reactions were positive at D7 (p<0.05). For WB spiked with type II parasites, all reactions remained positive at D7 but amplifications were significantly delayed from D2; and for WB spiked with RH strain, the proportion of positive reactions decreased at D7. Conclusion The storage of clinical samples at +4°C is compatible with the molecular detection of T. gondii parasites. Provided that PCR assays are performed in duplicate, storage of samples is possible up to 7 days. However, from the fifth day onwards, and for samples susceptible to contain low parasitic loads, we recommend to perform the PCR in multiplicate.
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Affiliation(s)
- Marie-Pierre Brenier-Pinchart
- Laboratoire de Parasitologie-Mycologie, CHU Grenoble Alpes et Institut pour l’Avancée des Biosciences (IAB), INSERM U1209-CNRS UMR 5309, Université Grenoble Alpes Grenoble, Grenoble, France
- Centre National de Référence Toxoplasmose-Pôle Biologie Moléculaire, France
- * E-mail:
| | - Emmanuelle Varlet-Marie
- Centre National de Référence Toxoplasmose-Pôle Biologie Moléculaire, France
- Université de Montpellier et Laboratoire de Parasitologie-Mycologie CHU Montpellier, Montpellier, France
| | - Florence Robert-Gangneux
- Centre National de Référence Toxoplasmose-Pôle Biologie Moléculaire, France
- CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé Environnement Travail), UMR_S 1085, Université de Rennes, Rennes, France
| | - Denis Filisetti
- Centre National de Référence Toxoplasmose-Pôle Biologie Moléculaire, France
- Institut de Parasitologie et de Pathologie Tropicale, Université de Strasbourg et Laboratoire de Parasitologie et Mycologie Médicale, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Juliette Guitard
- Centre National de Référence Toxoplasmose-Pôle Biologie Moléculaire, France
- Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Sorbonne Université, Paris, France
| | - Yvon Sterkers
- Centre National de Référence Toxoplasmose-Pôle Biologie Moléculaire, France
- CNRS, IRD, CHU de Montpellier, "MiVEGEC" et Laboratoire de Parasitologie-Mycologie, Université de Montpellier, Montpellier, France
| | - Hélène Yera
- Centre National de Référence Toxoplasmose-Pôle Biologie Moléculaire, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Cochin, Université de Paris, AP-HP, Paris, France
| | - Hervé Pelloux
- Laboratoire de Parasitologie-Mycologie, CHU Grenoble Alpes et Institut pour l’Avancée des Biosciences (IAB), INSERM U1209-CNRS UMR 5309, Université Grenoble Alpes Grenoble, Grenoble, France
- Centre National de Référence Toxoplasmose-Pôle Biologie Moléculaire, France
| | - Patrick Bastien
- Centre National de Référence Toxoplasmose-Pôle Biologie Moléculaire, France
- CNRS, IRD, CHU de Montpellier, "MiVEGEC" et Laboratoire de Parasitologie-Mycologie, Université de Montpellier, Montpellier, France
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Zhao H, Tang X, Wu M, Li Q, Yi X, Liu S, Jiang J, Wang S, Sun X. Transcriptome Characterization of Short Distance Transport Stress in Beef Cattle Blood. Front Genet 2021; 12:616388. [PMID: 33643382 PMCID: PMC7902800 DOI: 10.3389/fgene.2021.616388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/19/2021] [Indexed: 12/20/2022] Open
Abstract
The transportation is a crucial phase in beef cattle industry, and the annual losses caused by beef cattle transport stress are substantial. Several studies have described the effect of long distance transportation stress on animal health, such as disorder in nervous, endocrine, immune, and metabolic system. However, molecular mechanisms underlying short distance transportation stress is still poorly understood. Present study aims to investigate the effect of short distance transportation by measuring the hematological indices and transcriptomic analysis. In this study, a total 10 Qinchuan cattle were used to compare the molecular characteristics of blood before and after transportation. We have found that a stress-related marker "white blood cell count (WBC)" increased significantly after transportation. The decrease in triglyceride (TG), cholestenone (CHO), high-density lipoprotein (HDL), and low-density lipoprotein (LDL) showed that energy expenditure was increased after transportation, but not enough to activate fatty decomposition. Intriguingly, the decrease of malondialdehyde (MDA) showed that cattle were more resilience to oxidative stress. The RNA-seq showed that 1,092 differentially expressed genes (DEGs) were found (329 up-regulated and 763 down-regulated) between group before and group after. The GO and KEGG enrichment showed that the metabolic pathway and B cell function related pathways were enriched. Furthermore, median absolute deviation (MAD) top 5,000 genes were used to construct a co-expression network by weighted correlation network analysis (WGCNA), and 11 independent modules were identified. Combing with protein-protein interaction (PPI) analysis, the verification of quantitative real-time PCR (qPCR) and the correlation of B cell function, structural maintenance of chromosomes 3 (SMC3), jun proto-oncogene (JUN), and C-X-C motif chemokine ligand 10 (CXCL10) were suggested as potential molecular markers in identification of short distance transportation. Collectively, the blood RNA-seq analysis and WGCNA indicated that the disorder of B cell differentiation, proliferation, survival, and apoptosis were the potential molecular mechanism in short distance transportation stress. In conclusion, our results provide the novel insight about potential biomarkers for short distance transportation stress, which may serve as for diagnosing and preventing this condition in beef industry.
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Affiliation(s)
- Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoqin Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shirong Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Junyi Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,College of Grassland Agriculture, Northwest A&F University, Yangling, China
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Pal A, Gope A, Iannacchione G. Temperature and Concentration Dependence of Human Whole Blood and Protein Drying Droplets. Biomolecules 2021; 11:231. [PMID: 33562850 PMCID: PMC7915023 DOI: 10.3390/biom11020231] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022] Open
Abstract
The drying of bio-colloidal droplets can be used in many medical and forensic applications. The whole human blood is the most complex bio-colloid system, whereas bovine serum albumin (BSA) is the simplest. This paper focuses on the drying characteristics and the final morphology of these two bio-colloids. The experiments were conducted by varying their initial concentrations, and the solutions were dried under various controlled substrate temperatures using optical and scanning electron microscopy. The droplet parameters (the contact angle, the fluid front, and the first-order image statistics) reveal the drying process's unique features. Interestingly, both BSA and blood drying droplets' contact angle measurements show evidence of a concentration-driven transition as the behavior changes from non-monotonic to monotonic decrease. This result indicates that this transition behavior is not limited to multi-component bio-colloid (blood) only, but may be a phenomenon of a bio-colloidal solution containing a large number of interacting components. The high dilution of blood behaves like the BSA solution. The ring-like deposition, the crack morphology, and the microstructures suggest that the components have enough time to segregate and deposit onto the substrate under ambient conditions. However, there is insufficient time for evaporative-driven segregation to occur at elevated temperatures, as expected.
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Affiliation(s)
- Anusuya Pal
- Order-Disorder Phenomena Laboratory, Department of Physics, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
| | - Amalesh Gope
- Department of English, Tezpur University, Tezpur 784028, Assam, India;
| | - Germano Iannacchione
- Order-Disorder Phenomena Laboratory, Department of Physics, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
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Sotoudeh Anvari M, Gharib A, Abolhasani M, Azari-Yam A, Hossieni Gharalari F, Safavi M, Zare Mirzaie A, Vasei M. Pre-analytical Practices in the Molecular Diagnostic Tests, A Concise Review. IRANIAN JOURNAL OF PATHOLOGY 2020; 16:1-19. [PMID: 33391375 PMCID: PMC7691716 DOI: 10.30699/ijp.2020.124315.2357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/05/2020] [Indexed: 12/17/2022]
Abstract
Molecular assays for detection of nucleic acids in biologic specimens are valuable diagnostic tools supporting clinical diagnoses and therapeutic decisions. Pre-analytical errors, which occur before or during processing of nucleic acid extraction, contribute a significant role in common errors that take place in molecular laboratories. Certain practices in specimen collection, transportation, and storage can affect the integrity of nucleic acids before analysis. Applying best practices in these steps, helps to minimize those errors and leads to better decisions in patient diagnosis and treatment. Widely acceptable recommendations, which are for optimal molecular assays associated with pre-analytic variables, are limited. In this article, we have reviewed most of the important issues in sample handling from bed to bench before starting molecular tests, which can be used in diagnostic as well as research laboratories. We have addressed the most important pre-analytical points in performing molecular analysis in fixed and unfixed solid tissues, whole blood, serum, plasma, as well as most of the body fluids including urine, fecal and bronchial samples, as well as prenatal diagnosis samples.
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Affiliation(s)
- Maryam Sotoudeh Anvari
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Gharib
- Department of Pathology, Modarres Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abolhasani
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Aileen Azari-Yam
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Moeinadin Safavi
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zare Mirzaie
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vasei
- Cell-based Therapies Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Chen W, Wang T, Dou Z, Xie X. Self-Driven "Microfiltration" Enabled by Porous Superabsorbent Polymer (PSAP) Beads for Biofluid Specimen Processing and Storage. ACS MATERIALS LETTERS 2020; 2:1545-1554. [PMID: 33163968 PMCID: PMC7640703 DOI: 10.1021/acsmaterialslett.0c00348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/16/2020] [Indexed: 05/22/2023]
Abstract
A remote collection of biofluid specimens such as blood and urine remains a great challenge due to the requirement of continuous refrigeration. Without proper temperature regulation, the rapid degradation of analytical targets in the specimen may compromise the accuracy and reliability of the testing results. In this study, we develop porous superabsorbent polymer (PSAP) beads for fast and self-driven "microfiltration" of biofluid samples. This treatment effectively separates small analytical targets (e.g., glucose, catalase, and bacteriophage) and large undesired components (e.g., bacteria and blood cells) in the biofluids by capturing the former inside and excluding the latter outside the PSAP beads. We have successfully demonstrated that this treatment can reduce sample volume, self-aliquot the liquid sample, avoid microbial contamination, separate plasma from blood cells, stabilize target species inside the beads, and enable long-term storage at room temperature. Potential practical applications of this technology can provide an alternative sample collection and storage approach for medically underserved areas.
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Salzmann AP, Bamberg M, Courts C, Dørum G, Gosch A, Hadrys T, Hadzic G, Neis M, Schneider PM, Sijen T, den Berge MV, Wiegand P, Haas C. mRNA profiling of mock casework samples: Results of a FoRNAP collaborative exercise. Forensic Sci Int Genet 2020; 50:102409. [PMID: 33220528 DOI: 10.1016/j.fsigen.2020.102409] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/02/2020] [Accepted: 10/12/2020] [Indexed: 01/23/2023]
Abstract
In recent years, forensic mRNA profiling has increasingly been used to identify the origin of human body fluids. By now, several laboratories have implemented mRNA profiling and also use it in criminal casework. In 2018 the FoRNAP (Forensic RNA Profiling) group was established among a number of these laboratories with the aim of sharing experiences, discussing optimization potential, identifying challenges and suggesting solutions with regards to mRNA profiling and casework. To compare mRNA profiling methods and results a collaborative exercise was organized within the FoRNAP group. Seven laboratories from four countries received 16 stains, comprising six pure body fluid / tissue stains and ten mock casework samples. The laboratories were asked to analyze the provided stains with their in-house method (PCR/CE or MPS) and markers of choice. Five laboratories used a DNA/RNA co-extraction strategy. Overall, up to 11 mRNA markers per body fluid were analyzed. We found that mRNA profiling using different extraction and analysis methods as well as different multiplexes can be applied to casework-like samples. In general, high input samples were typed with high accuracy by all laboratories, regardless of the method used. Irrespective of the analysis strategy, samples of low input or mixed stains were more challenging to analyze and interpret since, alike to DNA profiling, a higher number of markers dropped out and/or additional unexpected markers not consistent with the cell type in question were detected. It could be shown that a plethora of different but valid analysis and interpretation strategies exist and are successfully applied in the Forensic Genetics community. Nevertheless, efforts aiming at optimizing and harmonizing interpretation approaches in order to achieve a higher consistency between laboratories might be desirable in the future. The simultaneous extraction of DNA alongside RNA showed to be an effective approach to identify not only the body fluid present but also to identify the donor(s) of the stain. This allows investigators to gain valuable information about the origin of crime scene samples and the course of events in a crime case.
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Affiliation(s)
| | - Malte Bamberg
- Institute of Legal Medicine, University Hospital, University of Ulm, Germany
| | - Cornelius Courts
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Annica Gosch
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office, Institute of Forensic Sciences, Munich, Germany
| | | | - Maximilian Neis
- Institute of Legal Medicine, Faculty of Medicine, University Hospital, University of Cologne, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University Hospital, University of Cologne, Germany
| | - Titia Sijen
- Netherlands Forensic Institute, The Hague, the Netherlands
| | | | - Peter Wiegand
- Institute of Legal Medicine, University Hospital, University of Ulm, Germany
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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Iyer GR, Hasan Q. Alteration of methylation status in archival DNA samples: A qualitative assessment by methylation specific polymerase chain reaction. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:837-842. [PMID: 32649027 DOI: 10.1002/em.22398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/25/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is an epigenetic mechanism that regulates gene expression, which also facilitates genomic imprinting. Genomic imprinting is responsible for differential expression of genes based on parent of origin. Altered methylation of parental alleles results in imprinting disorders diagnosed by methylation specific polymerase chain reaction (MS-PCR) technique. With increasing evidence of genes under epigenetic influence, methylation studies are extensively performed on archival samples. To evaluate effect of storage and storage conditions on DNA methylation, a systematic MS-PCR based analysis was planned on an imprinted gene, SNRPN, located on chromosome 15q11.2. It was assessed by MS-PCR on fresh, 4 -20, and -80°C stored DNA samples for different time periods for systematic evaluation of methylation status. Technical factors like type of sample processing, method of DNA isolation, primer region polymorphism, sample heterogeneity were also evaluated. DNA methylation was observed to be altered for SNRPN gene after storage at -80°C from 2 months onwards. Long-term storage of DNA at -80°C results in altered DNA methylation status. This may lead to false MS-PCR diagnosis of imprinting disorders. Our proof of concept study should be followed with quantitative validation since the findings have critical implications in the present era of biobanking.
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Affiliation(s)
- Gayatri Rangarajan Iyer
- Department of Genetics & Molecular Medicine, Kamineni Hospitals, LB Nagar, Hyderabad, India
- Department of Genetics, Osmania University, Tarnaka, Hyderabad, India
| | - Qurratulain Hasan
- Department of Genetics & Molecular Medicine, Kamineni Hospitals, LB Nagar, Hyderabad, India
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Kolluri N, Albarran N, Fan A, Olson A, Sagar M, Young A, Gomez-Marquez J, Klapperich CM. SNAPflex: a paper-and-plastic device for instrument-free RNA and DNA extraction from whole blood. LAB ON A CHIP 2020; 20:3386-3398. [PMID: 32766666 DOI: 10.1039/d0lc00277a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nucleic acid amplification tests (NAATs), which amplify and detect pathogen nucleic acids, are vital methods to diagnose diseases, particularly in cases where patients exhibit low levels of infection. For many blood-borne pathogens such as HIV or Plasmodium falciparum, it is necessary to first extract pathogen RNA or DNA from patient blood prior to NAAT analysis. Traditional nucleic acid extraction methods are expensive, resource-intensive and are often difficult to deploy to resource-limited areas where many blood-borne infections are widespread. Here, we describe a portable, paper-and-plastic device, called SNAPflex, for instrument-free nucleic acid extraction from whole blood, which builds upon our previous work for RNA extraction using a pressure-driven extraction system. SNAPflex shows improved HIV RNA extraction from simulated patient samples compared to traditional extraction methods as well as long-term stability of extracted RNA without the need for cold storage. We further demonstrated successful extraction and recovery of P. falciparum DNA from cultured parasites in whole blood. SNAPflex was designed to be easily manufacturable and deployable to resource-limited settings.
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Affiliation(s)
- Nikunja Kolluri
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.
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Meggendorfer M, Walter W, Haferlach T. WGS and WTS in leukaemia: A tool for diagnostics? Best Pract Res Clin Haematol 2020; 33:101190. [DOI: 10.1016/j.beha.2020.101190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
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50
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RNA isolation efficacy of commercial and modified conventional methods for Citrus tristeza virus and mRNA internal control amplification. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-019-00405-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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