About: Enrichment of Retroviral Sequences in Brain Tissue from Patients with Severe Demyelinating Diseases

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Enrichment of Retroviral Sequences in Brain Tissue from Patients with Severe Demyelinating Diseases
Creator	Wilson, T Bhetariya, P Chan, B Fischer, K Kriesel, J
Source	Medline; PMC
abstract	BACKGROUND: Our group has used deep sequencing to identify viral RNA signatures in human brain specimens. We have previously used this method to detect HSV1, GBV-C, and measles virus sequence in brain tissue from deceased donors. Deep sequencing was performed on brain specimens from a cohort of patients who died with progressive forms of MS, revealing evidence of increased expression of some human endogenous retrovirus (HERV) domains. OBJECTIVES: Identify RNA sequences and new antigens involved in the pathogenesis of MS METHODS: Deep sequencing was performed on RNA extracted from 12 progressive MS, 2 neuromyelitis optica (MS/NMO = demyelination group), 14 normal control, and 7 other neurologic disease (OND) control frozen brain specimens. The resulting single-ended 50 bp sequences (reads) were compared to a non redundant viral database representing (NRVDB) all 1.2 M viral records in GenBank. A retroviral gene catalog (RVGC) was prepared by identifying human genetic loci (GRCh37.p13) homologous to domains contained in the Gypsy 2.0 retro element database. Reads were aligned to the RVGC and human transcriptome with Bowtie2. The resulting viral hit rates (VHRs) were normalized by the number of high quality reads. The expression of human genes, including HERVs, was determined using Cufflinks. Comparisons between the groups were performed using the false discovery rate. RESULTS: Fifty to 131 million high quality reads per specimen were obtained. Comparison of the reads to the NRVDB suggested that the demyelination and OND specimens had higher VHRs against some retroviral sequences compared with the controls. This was confirmed by retroviral domain averaging. Gene expression analysis showed differential expression among some HERV sequences. Single read mapping revealed one envelope and one reverse transcriptase sequence record that were significantly enriched among the demyelination samples compared to the normal controls. Less restrictive (comprehensive) read mapping showed that 2 integrase, 2 core, 2 envelope, and 3 KRAB sequences that were overexpressed in the demyelination group. CONCLUSIONS: These data demonstrate that some endogenous retroviral sequences are significantly overexpressed in these demyelination brain tissue specimens, but the magnitude of this overexpression is small. This is consistent with the concept of HERV activation as a part of the innate immune response.
has issue date	2017-07-16(xsd:dateTime)
bibo:doi	10.16966/2473-1846.132
bibo:pmid	29202119
has license	cc-by
sha1sum (hex)	471711362b8adb4bda402d22aebd264f63f8e1b7
schema:url	https://doi.org/10.16966/2473-1846.132
resource representing a document's title	Enrichment of Retroviral Sequences in Brain Tissue from Patients with Severe Demyelinating Diseases
has PubMed Central identifier	PMC5707126
has PubMed identifier	29202119
schema:publication	J Emerg Dis Virol
resource representing a document's body	covid:471711362b8adb4bda402d22aebd264f63f8e1b7#body_text
is schema:about of	named entity 'brain tissue' named entity 'human brain' named entity 'DEMYELINATING DISEASES' named entity 'TO DETECT' named entity 'EVIDENCE OF' named entity 'DIED' named entity 'GROUP' named entity 'PROGRESSIVE' named entity 'HUMAN ENDOGENOUS RETROVIRUS' named entity 'FORMS' named entity 'MEASLES VIRUS' named entity 'BRAIN' named entity 'SPECIMENS' named entity 'GBV-C' named entity 'DECEASED' named entity 'SEVERE' named entity 'RETROVIRAL' named entity 'USED' named entity 'COHORT' named entity 'BRAIN TISSUE' named entity 'VIRAL RNA' named entity 'SIGNATURES' named entity 'BRAIN TISSUE' named entity 'ENRICHMENT' named entity 'HAVE' named entity 'HSV1' named entity 'BACKGROUND' named entity 'INCREASED EXPRESSION' named entity 'HUMAN' named entity 'SEQUENCES' named entity 'PATIENTS' named entity 'PERFORMED' named entity 'TO IDENTIFY' named entity 'PREVIOUSLY' named entity 'PATIENTS' named entity 'VIRUS SEQUENCE' named entity 'DEEP SEQUENCING' named entity 'METHOD' named entity 'REVEALING' named entity 'OUR' named entity 'DONORS' covid:arg/471711362b8adb4bda402d22aebd264f63f8e1b7 named entity 'HSV1' named entity 'donors' named entity 'signatures' named entity 'GBV-C' named entity 'HSV1' named entity 'viral RNA' named entity 'domains' named entity 'University of Colorado, Denver' named entity 'retroviral' named entity 'NMO' named entity 'demyelination' named entity 'evolution' named entity 'HSV' named entity 'HSV' named entity 'HIV-1' named entity 'demyelination' named entity 'HERV' named entity 'herpes viruses' named entity 'AIDS' named entity 'HSV' named entity 'JSRV' named entity 'retroviral' named entity 'bocavirus' named entity 'Illumina' named entity 'demyelination' named entity 'RNA' named entity 'RNA' named entity 'human genome' named entity 'RNA' named entity 'demyelination' named entity 'hepatitis' named entity 'NL63' named entity 'transposon' named entity 'exogenous' named entity 'multiple comparisons'

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