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  1. Article: Transposable element RNA dysregulation in mutant KRAS(G12C) 3D lung cancer spheroids.

    Carrillo, David / Reggiardo, Roman E / Lim, John / Mantalas, Gary / Peddu, Vikas / Kim, Daniel H

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Mutant KRAS regulates transposable element (TE) RNA and interferon-stimulated gene (ISG) expression, but it remains unclear whether diverse mutations in KRAS affect different TE RNAs throughout the genome. We analyzed the transcriptomes of 3D human lung ... ...

    Abstract Mutant KRAS regulates transposable element (TE) RNA and interferon-stimulated gene (ISG) expression, but it remains unclear whether diverse mutations in KRAS affect different TE RNAs throughout the genome. We analyzed the transcriptomes of 3D human lung cancer spheroids that harbor KRAS(G12C) mutations to determine the landscape of TE RNAs regulated by mutant KRAS(G12C). We found that KRAS(G12C) signaling is required for the expression of LINE- and LTR-derived TE RNAs that are distinct from TE RNAs previously shown to be regulated by mutant KRAS(G12D) or KRAS(G12V). Moreover, KRAS(G12C) inhibition specifically upregulates SINE-derived TE RNAs from the youngest Alu subfamily AluY. Our results reveal that TE RNA dysregulation in KRAS-driven lung cancer cells is mutation-dependent, while also highlighting a subset of young, Alu-derived TE RNAs that are coordinately activated with innate immunity genes upon KRAS(G12C) inhibition.
    Language English
    Publishing date 2023-02-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.27.530369
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Stability of SARS-CoV-2 in Phosphate-Buffered Saline for Molecular Detection.

    Perchetti, Garrett A / Huang, Meei-Li / Peddu, Vikas / Jerome, Keith R / Greninger, Alexander L

    Journal of clinical microbiology

    2020  Volume 58, Issue 8

    MeSH term(s) Betacoronavirus/isolation & purification ; Buffers ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Coronavirus Infections/diagnosis ; Microbial Viability/drug effects ; RNA, Viral/genetics ; RNA, Viral/isolation & purification ; SARS-CoV-2 ; Saline Solution ; Specimen Handling/methods
    Chemical Substances Buffers ; RNA, Viral ; Saline Solution
    Keywords covid19
    Language English
    Publishing date 2020-07-23
    Publishing country United States
    Document type Letter
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.01094-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1188: Show issues Location:
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  3. Article ; Online: Sensitive Recovery of Complete SARS-CoV-2 Genomes from Clinical Samples by Use of Swift Biosciences' SARS-CoV-2 Multiplex Amplicon Sequencing Panel.

    Addetia, Amin / Lin, Michelle J / Peddu, Vikas / Roychoudhury, Pavitra / Jerome, Keith R / Greninger, Alexander L

    Journal of clinical microbiology

    2020  Volume 59, Issue 1

    MeSH term(s) COVID-19/diagnosis ; COVID-19 Nucleic Acid Testing/methods ; Gene Library ; Genome, Viral/genetics ; Humans ; Phylogeny ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Whole Genome Sequencing/methods
    Chemical Substances RNA, Viral
    Keywords covid19
    Language English
    Publishing date 2020-12-17
    Publishing country United States
    Document type Evaluation Study ; Letter
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.02226-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  4. Article ; Online: Profiling of repetitive RNA sequences in the blood plasma of patients with cancer.

    Reggiardo, Roman E / Maroli, Sreelakshmi Velandi / Peddu, Vikas / Davidson, Andrew E / Hill, Alexander / LaMontagne, Erin / Aaraj, Yassmin Al / Jain, Miten / Chan, Stephen Y / Kim, Daniel H

    Nature biomedical engineering

    2023  Volume 7, Issue 12, Page(s) 1627–1635

    Abstract: Liquid biopsies provide a means for the profiling of cell-free RNAs secreted by cells throughout the body. Although well-annotated coding and non-coding transcripts in blood are readily detectable and can serve as biomarkers of disease, the overall ... ...

    Abstract Liquid biopsies provide a means for the profiling of cell-free RNAs secreted by cells throughout the body. Although well-annotated coding and non-coding transcripts in blood are readily detectable and can serve as biomarkers of disease, the overall diagnostic utility of the cell-free transcriptome remains unclear. Here we show that RNAs derived from transposable elements and other repeat elements are enriched in the cell-free transcriptome of patients with cancer, and that they serve as signatures for the accurate classification of the disease. We used repeat-element-aware liquid-biopsy technology and single-molecule nanopore sequencing to profile the cell-free transcriptome in plasma from patients with cancer and to examine millions of genomic features comprising all annotated genes and repeat elements throughout the genome. By aggregating individual repeat elements to the subfamily level, we found that samples with pancreatic cancer are enriched with specific Alu subfamilies, whereas other cancers have their own characteristic cell-free RNA profile. Our findings show that repetitive RNA sequences are abundant in blood and can be used as disease-specific diagnostic biomarkers.
    MeSH term(s) Humans ; RNA/genetics ; Base Sequence ; DNA Transposable Elements ; Plasma ; Neoplasms/diagnosis ; Neoplasms/genetics ; Biomarkers
    Chemical Substances RNA (63231-63-0) ; DNA Transposable Elements ; Biomarkers
    Language English
    Publishing date 2023-08-31
    Publishing country England
    Document type Journal Article
    ISSN 2157-846X
    ISSN (online) 2157-846X
    DOI 10.1038/s41551-023-01081-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Stability of SARS-CoV-2 in Phosphate-Buffered Saline for Molecular Detection

    Perchetti, Garrett A / Huang, Meei-Li / Peddu, Vikas / Jerome, Keith R / Greninger, Alexander L

    J. clin. microbiol

    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #710406
    Database COVID19

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  6. Article: Sensitive recovery of complete SARS-CoV-2 genomes from clinical samples using Swift Biosciences' SARS-CoV-2 multiplex amplicon sequencing panel

    Addetia, Amin / Lin, Michelle J / Peddu, Vikas / Roychoudhury, Pavitra / Jerome, Keith R / Greninger, Alexander L

    J. clin. microbiol

    Abstract: Whole genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a better understanding of the virus's origin, transmission, and evolution (1-6). . ...

    Abstract Whole genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a better understanding of the virus's origin, transmission, and evolution (1-6). .
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #852548
    Database COVID19

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  7. Article: Stability of SARS-CoV-2 in PBS for Molecular Detection

    Perchetti, Garrett A / Huang, Meei-Li / Peddu, Vikas / Jerome, Keith R / Greninger, Alexander L

    J. clin. microbiol

    Abstract: RNA viruses often require "cold-chains" of transportation to prevent the breakdown of genetic material. . ...

    Abstract RNA viruses often require "cold-chains" of transportation to prevent the breakdown of genetic material. .
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #32414839
    Database COVID19

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    Inter-library loan at ZB MED

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  8. Article ; Online: Sensitive recovery of complete SARS-CoV-2 genomes from clinical samples using Swift Biosciences' SARS-CoV-2 multiplex amplicon sequencing panel

    Addetia, Amin / Lin, Michelle J. / Peddu, Vikas / Roychoudhury, Pavitra / Jerome, Keith R. / Greninger, Alexander L.

    Journal of Clinical Microbiology ; ISSN 0095-1137 1098-660X

    2020  

    Abstract: Whole genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a better understanding of the virus's origin, transmission, and evolution (1-6).… ...

    Abstract Whole genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a better understanding of the virus's origin, transmission, and evolution (1-6).…
    Keywords Microbiology (medical) ; covid19
    Language English
    Publisher American Society for Microbiology
    Publishing country us
    Document type Article ; Online
    DOI 10.1128/jcm.02226-20
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Stability of SARS-CoV-2 in Phosphate-Buffered Saline for Molecular Detection

    Perchetti, Garrett A. / Huang, Meei-Li / Peddu, Vikas / Jerome, Keith R. / Greninger, Alexander L.

    Journal of Clinical Microbiology

    2020  Volume 58, Issue 8

    Keywords Microbiology (medical) ; covid19
    Language English
    Publisher American Society for Microbiology
    Publishing country us
    Document type Article ; Online
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.01094-20
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1188: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  10. Article ; Online: Host-pathogen dynamics in longitudinal clinical specimens from patients with COVID-19.

    Lin, Michelle J / Rachleff, Victoria M / Xie, Hong / Shrestha, Lasata / Lieberman, Nicole A P / Peddu, Vikas / Addetia, Amin / Casto, Amanda M / Breit, Nathan / Mathias, Patrick C / Huang, Meei-Li / Jerome, Keith R / Greninger, Alexander L / Roychoudhury, Pavitra

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 5856

    Abstract: Rapid dissemination of SARS-CoV-2 sequencing data to public repositories has enabled widespread study of viral genomes, but studies of longitudinal specimens from infected persons are relatively limited. Analysis of longitudinal specimens enables ... ...

    Abstract Rapid dissemination of SARS-CoV-2 sequencing data to public repositories has enabled widespread study of viral genomes, but studies of longitudinal specimens from infected persons are relatively limited. Analysis of longitudinal specimens enables understanding of how host immune pressures drive viral evolution in vivo. Here we performed sequencing of 49 longitudinal SARS-CoV-2-positive samples from 20 patients in Washington State collected between March and September of 2020. Viral loads declined over time with an average increase in RT-QPCR cycle threshold of 0.87 per day. We found that there was negligible change in SARS-CoV-2 consensus sequences over time, but identified a number of nonsynonymous variants at low frequencies across the genome. We observed enrichment for a relatively small number of these variants, all of which are now seen in consensus genomes across the globe at low prevalence. In one patient, we saw rapid emergence of various low-level deletion variants at the N-terminal domain of the spike glycoprotein, some of which have previously been shown to be associated with reduced neutralization potency from sera. In a subset of samples that were sequenced using metagenomic methods, differential gene expression analysis showed a downregulation of cytoskeletal genes that was consistent with a loss of ciliated epithelium during infection and recovery. We also identified co-occurrence of bacterial species in samples from multiple hospitalized individuals. These results demonstrate that the intrahost genetic composition of SARS-CoV-2 is dynamic during the course of COVID-19, and highlight the need for continued surveillance and deep sequencing of minor variants.
    MeSH term(s) COVID-19/genetics ; Genome, Viral ; Humans ; Metagenome ; Metagenomics ; SARS-CoV-2/genetics
    Language English
    Publishing date 2022-04-07
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-09752-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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