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Walker JE, Oliver JC, Stewart AM, Beh ST, Arce RA, Glass MJ, Vargas DE, Qiji SH, Intorcia AJ, Borja CI, Cline MP, Hemmingsen SJ, Krupp AN, McHattie RD, Mariner MR, Lorenzini I, Aslam S, Tremblay C, Beach TG, Serrano GE. Measuring Up: A Comparison of TapeStation 4200 and Bioanalyzer 2100 as Measurement Tools for RNA Quality in Postmortem Human Brain Samples. Int J Mol Sci 2023; 24:13795. [PMID: 37762097 PMCID: PMC10531353 DOI: 10.3390/ijms241813795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The determination of RNA integrity is a critical quality assessment tool for gene expression studies where the experiment's success is highly dependent on the sample quality. Since its introduction in 1999, the gold standard in the scientific community has been the Agilent 2100 Bioanalyzer's RNA integrity number (RIN), which uses a 1-10 value system, from 1 being the most degraded, to 10 being the most intact. In 2015, Agilent launched 4200 TapeStation's RIN equivalent, and reported a strong correlation of r2 of 0.936 and a median error < ±0.4 RIN units. To evaluate this claim, we compared the Agilent 4200 TapeStation's RIN equivalent (RINe) and DV200 to the Agilent 2100 Bioanalyzer's RIN for 183 parallel RNA samples. In our study, using RNA from a total of 183 human postmortem brain samples, we found that the RIN and RINe values only weakly correlate, with an r2 of 0.393 and an average difference of 3.2 RIN units. DV200 also only weakly correlated with RIN (r2 of 0.182) and RINe (r2 of 0.347). Finally, when applying a cut-off value of 6.5 for both metrics, we found that 95.6% of samples passed with RIN, while only 23.5% passed with RINe. Our results suggest that even though RIN (Bioanalyzer) and RINe (TapeStation) use the same 1-10 value system, they should not be used interchangeably, and cut-off values should be calculated independently.
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Walker JE, Oliver JC, Stewart AM, Beh ST, Arce RA, Glass MJ, Vargas DE, Qiji SH, Intorcia AJ, Borja CI, Cline MP, Hemmingsen SJ, Krupp AN, McHattie RD, Mariner MR, Lorenzini I, Aslam S, Tremblay C, Beach TG, Serrano GE. Measuring up: A Comparison of Tapestation 4200 and Bioanalyzer 2100 as Measurement Tools for RNA Quality in Postmortem Human Brain Samples. medRxiv 2023:2023.07.03.23291969. [PMID: 37461632 PMCID: PMC10350153 DOI: 10.1101/2023.07.03.23291969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Determining RNA integrity is a critical quality assessment tool for gene expression studies where the experiment's success is highly dependent on sample quality. Since its introduction in 1999, the gold standard in the scientific community has been the Agilent 2100 Bioanalyzer's RNA Integrity Number (RIN) which uses a 1-10 value system with 1 being the most degraded to 10 being the most intact. In 2015, Agilent launched the 4200 Tapestation's RIN equivalent and reported a strong correlation of r 2 of 0.936 and median error < ± 0.4 RIN units. To evaluate this claim, we compared the Agilent 4200 Tapestation's RIN equivalent (RINe) and DV200 to the Agilent 2100 Bioanalyzer's RIN for 183 parallel RNA samples. In our study, using RNA from a total of 183 human postmortem brain samples, we found that the RIN and RINe values only weakly correlate with an r 2 of 0.393 and an average difference of 3.2 RIN units. DV200 also only weakly correlated with RIN (r 2 of 0.182) and RINe (r 2 of 0.347). Finally, when applying a cut-off value of 6.5 for both metrics, we found that 95.6% of samples passed with RIN, while only 23.5% passed with RINe. Our results suggest that even though RIN (Bioanalyzer) and RINe (Tapestation) use the same 1-10 value system, they should not be used interchangeably, and cut-off values should be calculated independently.
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Beach TG, Sue LI, Scott S, Intorcia AJ, Walker JE, Arce RA, Glass MJ, Borja CI, Cline MP, Hemmingsen SJ, Qiji S, Stewart A, Martinez KN, Krupp A, McHattie R, Mariner M, Lorenzini I, Kuramoto A, Long KE, Tremblay C, Caselli RJ, Woodruff BK, Rapscak SZ, Belden CM, Goldfarb D, Choudhury P, Driver-Dunckley ED, Mehta SH, Sabbagh MN, Shill HA, Atri A, Adler CH, Serrano GE. Cerebral white matter rarefaction has both neurodegenerative and vascular causes and may primarily be a distal axonopathy. J Neuropathol Exp Neurol 2023; 82:457-466. [PMID: 37071794 PMCID: PMC10209646 DOI: 10.1093/jnen/nlad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Cerebral white matter rarefaction (CWMR) was considered by Binswanger and Alzheimer to be due to cerebral arteriolosclerosis. Renewed attention came with CT and MR brain imaging, and neuropathological studies finding a high rate of CWMR in Alzheimer disease (AD). The relative contributions of cerebrovascular disease and AD to CWMR are still uncertain. In 1181 autopsies by the Arizona Study of Aging and Neurodegenerative Disorders (AZSAND), large-format brain sections were used to grade CWMR and determine its vascular and neurodegenerative correlates. Almost all neurodegenerative diseases had more severe CWMR than the normal control group. Multivariable logistic regression models indicated that Braak neurofibrillary stage was the strongest predictor of CWMR, with additional independently significant predictors including age, cortical and diencephalic lacunar and microinfarcts, body mass index, and female sex. It appears that while AD and cerebrovascular pathology may be additive in causing CWMR, both may be solely capable of this. The typical periventricular pattern suggests that CWMR is primarily a distal axonopathy caused by dysfunction of the cell bodies of long-association corticocortical projection neurons. A consequence of these findings is that CWMR should not be viewed simply as "small vessel disease" or as a pathognomonic indicator of vascular cognitive impairment or vascular dementia.
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Affiliation(s)
- Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Lucia I Sue
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Sarah Scott
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | - Richard A Arce
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Michael J Glass
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Madison P Cline
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Sanaria Qiji
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Analisa Stewart
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Addison Krupp
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Rylee McHattie
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Monica Mariner
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Angela Kuramoto
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Kathy E Long
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | | | | | | | | | | | | | - Shyamal H Mehta
- Department of Neurology, Mayo Clinic, Scottsdale, Arizona, USA
| | | | - Holly A Shill
- Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Alireza Atri
- Banner Sun Health Research Institute, Sun City, Arizona, USA
- Harvard Medical School & Brigham & Women’s Hospital, Boston, Massachusetts, USA
| | - Charles H Adler
- Department of Neurology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona, USA
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Serrano GE, Walker JE, Tremblay C, Piras IS, Huentelman MJ, Belden CM, Goldfarb D, Shprecher D, Atri A, Adler CH, Shill HA, Driver-Dunckley E, Mehta SH, Caselli R, Woodruff BK, Haarer CF, Ruhlen T, Torres M, Nguyen S, Schmitt D, Rapscak SZ, Bime C, Peters JL, Alevritis E, Arce RA, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Oliver J, Russell A, Suszczewicz KE, Borja CI, Cline MP, Hemmingsen SJ, Qiji S, Hobgood HM, Mizgerd JP, Sahoo MK, Zhang H, Solis D, Montine TJ, Berry GJ, Reiman EM, Röltgen K, Boyd SD, Pinsky BA, Zehnder JL, Talbot P, Desforges M, DeTure M, Dickson DW, Beach TG. SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19. J Neuropathol Exp Neurol 2022; 81:666-695. [PMID: 35818336 PMCID: PMC9278252 DOI: 10.1093/jnen/nlac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Brains of 42 COVID-19 decedents and 107 non-COVID-19 controls were studied. RT-PCR screening of 16 regions from 20 COVID-19 autopsies found SARS-CoV-2 E gene viral sequences in 7 regions (2.5% of 320 samples), concentrated in 4/20 subjects (20%). Additional screening of olfactory bulb (OB), amygdala (AMY) and entorhinal area for E, N1, N2, RNA-dependent RNA polymerase, and S gene sequences detected one or more of these in OB in 8/21 subjects (38%). It is uncertain whether these RNA sequences represent viable virus. Significant histopathology was limited to 2/42 cases (4.8%), one with a large acute cerebral infarct and one with hemorrhagic encephalitis. Case-control RNAseq in OB and AMY found more than 5000 and 700 differentially expressed genes, respectively, unrelated to RT-PCR results; these involved immune response, neuronal constituents, and olfactory/taste receptor genes. Olfactory marker protein-1 reduction indicated COVID-19-related loss of OB olfactory mucosa afferents. Iba-1-immunoreactive microglia had reduced area fractions in cerebellar cortex and AMY, and cytokine arrays showed generalized downregulation in AMY and upregulation in blood serum in COVID-19 cases. Although OB is a major brain portal for SARS-CoV-2, COVID-19 brain changes are more likely due to blood-borne immune mediators and trans-synaptic gene expression changes arising from OB deafferentation.
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Affiliation(s)
- Geidy E Serrano
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Jessica E Walker
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Cécilia Tremblay
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | - Danielle Goldfarb
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - David Shprecher
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Alireza Atri
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA.,Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Charles H Adler
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Holly A Shill
- Barrow Neurological Institute, Phoenix, Arizona, USA
| | | | - Shyamal H Mehta
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Richard Caselli
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Bryan K Woodruff
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | | | - Thomas Ruhlen
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Maria Torres
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Steve Nguyen
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Dasan Schmitt
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | | | | | | | | | - Richard A Arce
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Michael J Glass
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Daisy Vargas
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Lucia I Sue
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Courtney M Nelson
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Javon Oliver
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Aryck Russell
- Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | | | - Claryssa I Borja
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Madison P Cline
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Sanaria Qiji
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Holly M Hobgood
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Haiyu Zhang
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Daniel Solis
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, California, USA.,From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Stanford, California, USA.,Division of Infectious Disease & Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pierre Talbot
- Laboratory of Neuroimmunology, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Marc Desforges
- Laboratory of Virology, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada.,Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Michael DeTure
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Dennis W Dickson
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Thomas G Beach
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
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5
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Serrano GE, Walker JE, Arce R, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Oliver J, Papa J, Russell A, Suszczewicz KE, Borja CI, Belden C, Goldfarb D, Shprecher D, Atri A, Adler CH, Shill HA, Driver-Dunckley E, Mehta SH, Readhead B, Huentelman MJ, Peters JL, Alevritis E, Bimi C, Mizgerd JP, Reiman EM, Montine TJ, Desforges M, Zehnder JL, Sahoo MK, Zhang H, Solis D, Pinsky BA, Deture M, Dickson DW, Beach TG. Mapping of SARS-CoV-2 Brain Invasion and Histopathology in COVID-19 Disease. medRxiv 2021:2021.02.15.21251511. [PMID: 33619496 PMCID: PMC7899461 DOI: 10.1101/2021.02.15.21251511] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The coronavirus SARS-CoV-2 (SCV2) causes acute respiratory distress, termed COVID-19 disease, with substantial morbidity and mortality. As SCV2 is related to previously-studied coronaviruses that have been shown to have the capability for brain invasion, it seems likely that SCV2 may be able to do so as well. To date, although there have been many clinical and autopsy-based reports that describe a broad range of SCV2-associated neurological conditions, it is unclear what fraction of these have been due to direct CNS invasion versus indirect effects caused by systemic reactions to critical illness. Still critically lacking is a comprehensive tissue-based survey of the CNS presence and specific neuropathology of SCV2 in humans. We conducted an extensive neuroanatomical survey of RT-PCR-detected SCV2 in 16 brain regions from 20 subjects who died of COVID-19 disease. Targeted areas were those with cranial nerve nuclei, including the olfactory bulb, medullary dorsal motor nucleus of the vagus nerve and the pontine trigeminal nerve nuclei, as well as areas possibly exposed to hematogenous entry, including the choroid plexus, leptomeninges, median eminence of the hypothalamus and area postrema of the medulla. Subjects ranged in age from 38 to 97 (mean 77) with 9 females and 11 males. Most subjects had typical age-related neuropathological findings. Two subjects had severe neuropathology, one with a large acute cerebral infarction and one with hemorrhagic encephalitis, that was unequivocally related to their COVID-19 disease while most of the 18 other subjects had non-specific histopathology including focal β-amyloid precursor protein white matter immunoreactivity and sparse perivascular mononuclear cell cuffing. Four subjects (20%) had SCV2 RNA in one or more brain regions including the olfactory bulb, amygdala, entorhinal area, temporal and frontal neocortex, dorsal medulla and leptomeninges. The subject with encephalitis was SCV2-positive in a histopathologically-affected area, the entorhinal cortex, while the subject with the large acute cerebral infarct was SCV2-negative in all brain regions. Like other human coronaviruses, SCV2 can inflict acute neuropathology in susceptible patients. Much remains to be understood, including what viral and host factors influence SCV2 brain invasion and whether it is cleared from the brain subsequent to the acute illness.
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Affiliation(s)
| | | | - Richard Arce
- Banner Sun Health Research Institute, Sun City, AZ
| | | | - Daisy Vargas
- Banner Sun Health Research Institute, Sun City, AZ
| | - Lucia I. Sue
- Banner Sun Health Research Institute, Sun City, AZ
| | | | | | - Javon Oliver
- Banner Sun Health Research Institute, Sun City, AZ
| | - Jaclyn Papa
- Banner Sun Health Research Institute, Sun City, AZ
| | | | | | | | | | | | | | - Alireza Atri
- Banner Sun Health Research Institute, Sun City, AZ
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Charles H. Adler
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ
| | | | | | - Shyamal H. Mehta
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ
| | - Benjamin Readhead
- Arizona State University-Banner Neurodegenerative Disease Research Center, Tempe, AZ
| | | | | | | | | | | | | | - Thomas J. Montine
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Marc Desforges
- Centre Hospitalier Universitaire Sainte-Justine, Laboratory of Virology, Montreal, Canada
| | - James L. Zehnder
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Malaya K. Sahoo
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Haiyu Zhang
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Daniel Solis
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Benjamin A. Pinsky
- Stanford University Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford, CA
| | - Michael Deture
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville FL
| | - Dennis W. Dickson
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville FL
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