scholarly journals Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses

Apmis ◽  
2016 ◽  
Vol 124 (1-2) ◽  
pp. 127-139 ◽  
Author(s):  
Martin Sokol ◽  
Karen Margrethe Jessen ◽  
Finn Skou Pedersen
Keyword(s):  
Rna Sequencing ◽  
Endogenous Retroviruses ◽  
Next Generation ◽  
Human Endogenous Retroviruses

Expression of human endogenous retroviruses and associated transcripts in Hodgkin lymphoma cells

2020 ◽  
Author(s):  
K Engel ◽  
A Krüger ◽  
V Vandrey ◽  
J Schneider ◽  
I Volkmer ◽  
...  
Keyword(s):  
Hodgkin Lymphoma ◽  
Endogenous Retroviruses ◽  
Lymphoma Cells ◽  
Human Endogenous Retroviruses

Human endogenous retroviruses HERV-H, HERV-W and HERV-K in preeclampsia

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Massimiliano Bergallo ◽  
Pier-Angelo Tovo ◽  
Enrico Bertino ◽  
Valentina Daprà ◽  
Alice Pirra ◽  
...  
Keyword(s):  
Endogenous Retroviruses ◽  
Human Endogenous Retroviruses

scholarly journals Suitability of Bronchoscopic Biopsy Tissue Samples for Next-Generation Sequencing

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 391
Author(s):  
Shuji Murakami ◽  
Tomoyuki Yokose ◽  
Daiji Nemoto ◽  
Masaki Suzuki ◽  
Ryou Usui ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Success Rate ◽  
Rna Sequencing ◽  
Surface Area ◽  
Endobronchial Ultrasound ◽  
Next Generation ◽  
Endobronchial Ultrasonography ◽  
Tissue Surface ◽  
The Impact ◽  
Generation Sequencing

A sufficiently large tissue sample is required to perform next-generation sequencing (NGS) with a high success rate, but the majority of patients with advanced non-small-cell lung cancer (NSCLC) are diagnosed with small biopsy specimens. Biopsy samples were collected from 184 patients with bronchoscopically diagnosed NSCLC. The tissue surface area, tumor cell count, and tumor content rate of each biopsy sample were evaluated. The impact of the cut-off criteria for the tissue surface area (≥1 mm2) and tumor content rate (≥30%) on the success rate of the Oncomine Dx Target Test (ODxTT) was evaluated. The mean tissue surface area of the transbronchial biopsies was 1.23 ± 0.85 mm2 when small endobronchial ultrasonography with a guide sheath (EBUS-GS) was used, 2.16 ± 1.49 mm2 with large EBUS-GS, and 1.81 ± 0.75 mm2 with endobronchial biopsy (EBB). The proportion of samples with a tissue surface area of ≥1 mm2 was 48.8% for small EBUS-GS, 79.2% for large EBUS-GS, and 78.6% for EBB. Sixty-nine patients underwent ODxTT. The success rate of DNA sequencing was 84.1% and that of RNA sequencing was 92.7% over all patients. The success rate of DNA (RNA) sequencing was 57.1% (71.4%) for small EBUS-GS (n = 14), 93.4% (96.9%) for large EBUS-GS (n = 32), 62.5% (100%) for EBB (n = 8), and 100% (100%) for endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) (n = 15). Regardless of the device used, a tissue surface area of ≥ 1 mm2 is adequate for samples to be tested with NGS.

scholarly journals COVID-19 in Children: Expressions of Type I/II/III Interferons, TRIM28, SETDB1, and Endogenous Retroviruses in Mild and Severe Cases

2021 ◽  
Vol 22 (14) ◽  
pp. 7481
Author(s):  
Pier-Angelo Tovo ◽  
Silvia Garazzino ◽  
Valentina Daprà ◽  
Giulia Pruccoli ◽  
Cristina Calvi ◽  
...  
Keyword(s):  
Viral Infections ◽  
Severe Disease ◽  
Endogenous Retroviruses ◽  
Type I ◽  
Human Endogenous Retroviruses ◽  
Moderate Disease ◽  
Amplification Assay ◽  
Positive Correlations ◽  
Inducible Genes ◽  
Inflammatory Syndrome

Children with the new coronavirus disease 2019 (COVID-19) have milder symptoms and a better prognosis than adult patients. Several investigations assessed type I, II, and III interferon (IFN) signatures in SARS-CoV-2 infected adults, however no data are available for pediatric patients. RIM28 and SETDB1 regulate the transcription of multiple genes involved in the immune response as well as of human endogenous retroviruses (HERVs). Exogenous viral infections can trigger the activation of HERVs, which in turn can induce inflammatory and immune reactions. Despite the potential cross-talks between SARS-CoV-2 infection and TRIM28, SETDB1, and HERVs, information on their expressions in COVID-19 patients is lacking. We assessed, through a PCR real time Taqman amplification assay, the transcription levels of six IFN-I stimulated genes, IFN-II and three of its sensitive genes, three IFN-lIIs, as well as of TRIM28, SETDB1, pol genes of HERV-H, -K, and -W families, and of env genes of Syncytin (SYN)1, SYN2, and multiple sclerosis-associated retrovirus (MRSV) in peripheral blood from COVID-19 children nd in control uninfected subjects. Higher expression levels of IFN-I and IFN-II inducible genes were observed in 36 COVID-19-infected children with mild or moderate disease as compared to uninfected controls, whereas their concentrations decreased in 17 children with severe disease and in 11 with multisystem inflammatory syndrome (MIS-C). Similar findings were found for the expression of TRIM-28, SETDB1, and every HERV gene. Positive correlations emerged between the transcriptional levels of type I and II IFNs, TRIM28, SETDB1, and HERVs in COVID-19 patients. IFN-III expressions were comparable in each group of subjects. This preserved induction of IFN-λs could contribute to the better control of the infection in children as compared to adults, in whom IFN-III deficiency has been reported. The upregulation of IFN-I, IFN-II, TRIM28, SETDB1, and HERVs in children with mild symptoms, their declines in severe cases or with MIS-C, and the positive correlations of their transcription in SARS-CoV-2-infected children suggest that they may play important roles in conditioning the evolution of the infection.

scholarly journals Human Endogenous Retrovirus Reactivation: Implications for Cancer Immunotherapy

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1999
Author(s):  
Annacarmen Petrizzo ◽  
Concetta Ragone ◽  
Beatrice Cavalluzzo ◽  
Angela Mauriello ◽  
Carmen Manolio ◽  
...  
Keyword(s):  
Cancer Immunotherapy ◽  
Genetic Material ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retrovirus ◽  
Danger Signal ◽  
Human Endogenous Retroviruses ◽  
Double Stranded Rna ◽  
Specific Antigens ◽  
Viral Mimicry

Human endogenous retroviruses (HERVs) derive from ancestral exogenous retroviruses whose genetic material has been integrated in our germline DNA. Several lines of evidence indicate that cancer immunotherapy may benefit from HERV reactivation, which can be induced either by drugs or by cellular changes occurring in tumor cells. Indeed, several studies indicate that HERV proviral DNA can be transcribed either to double-stranded RNA (dsRNA) that is sensed as a “danger signal” by pattern recognition receptors (PRRs), leading to a viral mimicry state, or to mRNA that is translated into proteins that may contribute to the landscape of tumor-specific antigens (TSAs). Alternatively, HERV reactivation is associated with the expression of long noncoding RNAs (lncRNAs). In this review, we will highlight recent findings on HERV reactivation in cancer and its implications for cancer immunotherapy.

Regulation of human endogenous retroviruses of the W family by type III interferon λ2 and HIV in astrocytes

Cytokine ◽  
2009 ◽  
Vol 48 (1-2) ◽  
pp. 65
Author(s):  
Alessandra Mei ◽  
Giuseppe Mameli ◽  
Caterina Serra ◽  
Luciana Poddighe ◽  
Elena Uleriand ◽  
...  
Keyword(s):  
Endogenous Retroviruses ◽  
Human Endogenous Retroviruses ◽  
Type Iii ◽  
Type Iii Interferon

scholarly journals Aging-associated patterns in the expression of human endogenous retroviruses

PLoS ONE ◽  
2018 ◽  
Vol 13 (12) ◽  
pp. e0207407 ◽  
Author(s):  
Tapio Nevalainen ◽  
Arttu Autio ◽  
Binisha Hamal Mishra ◽  
Saara Marttila ◽  
Marja Jylhä ◽  
...  
Keyword(s):  
Endogenous Retroviruses ◽  
Human Endogenous Retroviruses

scholarly journals Gestational Psittacosis Resulting in Neonatal Death Identified by Next-Generation RNA Sequencing of Postmortem, Formalin-Fixed Lung Tissue

2018 ◽  
Vol 5 (8) ◽  
Author(s):  
Litty Paul ◽  
Jessica Comstock ◽  
Kornelia Edes ◽  
Robert Schlaberg
Keyword(s):  
Rna Sequencing ◽  
Infant Death ◽  
Neonatal Death ◽  
Pathogen Detection ◽  
Severe Disease ◽  
Adverse Outcomes ◽  
Premature Delivery ◽  
Next Generation ◽  
Death Studies ◽  
Formalin Fixed

Abstract Psittacosis is a rare zoonosis that can cause severe disease and adverse outcomes during pregnancy. We identified a previously elusive case of psittacosis causing premature delivery and infant death by next-generation RNA sequencing of postmortem tissues. Hypothesis-free pathogen detection in postmortem specimens can increase the yield of epidemiologic and cause-of-death studies.

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